@article {pmid41385173, year = {2025}, author = {Othman, AA and Mohamed Zain, NI and Eshak, Z and Adman, MA and Abd Latif, Z and Aboshanab, KM and Ahmad, A}, title = {Diversity of necrophagous flies and microbiome profiling of Phumosia promittens as a rainforest health indicator.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-025-01994-3}, pmid = {41385173}, issn = {2191-0855}, abstract = {Necrophagous flies play a critical role in decomposition and serve as bioindicators of environmental health and pollution. Malaysia's tropical rainforest ecosystems may host many necrophagous fly species, including unique blowflies and their associated bacteria. However, in many forest reserve areas, the diversity of these flies remains poorly studied. This study examines the diversity of necrophagous flies and their associated surface bacteria community, with a particular focus on Phumosia promittens (Walker in J Proc Linn Soc Lond Zool 4:90-96, 1859) in the Bangi Forest Reserve, Universiti Kebangsaan Malaysia. Sampling was conducted across three plots using baited traps, and collected flies were morphologically identified and processed under sterile conditions. Surface bacteria from P. promittens were isolated and analysed through metagenomic analysis targeting the 16S rRNA (V3-V4) amplicon sequencing gene to characterise their microbial communities comprehensively. Among 2,528 individuals collected, Chrysomya megacephala (Fabricius) was the most dominant species overall, while P. promittens was the most abundant among native forest species, suggesting their ecological adaptability and potential as a bioindicator of healthy rainforest. Shannon-Wiener and Simpson's diversity of flies in the study location were 0.67 ± 0.11 and 0.29 ± 0.06, respectively. Meanwhile, the Shannon-Wiener and Simpson's diversity of bacteria from P. promittens were 5.64 ± 0.70 and 0.96 ± 0.02, respectively. Bacterial microbiome analysis revealed the presence of core genera, including Wohlfahrtiimonas, Dysgonomonas, Vagococcus, and Ignatzschineria, which are implicated in both ecological symbiosis and public health concerns. These bacteria may contribute to nutrient cycling, such as heavy metals and antibiotics. Notably, several of these genera are emerging zoonotic pathogens with antimicrobial resistance, highlighting the dual role of necrophagous flies as ecosystem contributors and disease vectors. The findings underscore the importance of monitoring native fly species and their microbiota to assess the integrity of forest ecosystems and potential public health risks.}, } @article {pmid41384994, year = {2025}, author = {Zhang, J and Liu, J and Bayani, A}, title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.}, journal = {Journal of cancer research and clinical oncology}, volume = {152}, number = {1}, pages = {8}, pmid = {41384994}, issn = {1432-1335}, mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.}, } @article {pmid41381437, year = {2025}, author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J}, title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11067}, pmid = {41381437}, issn = {2041-1723}, mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth & development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; }, abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.}, } @article {pmid41381092, year = {2025}, author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM}, title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70261}, doi = {10.1111/1758-2229.70261}, pmid = {41381092}, issn = {1758-2229}, support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; }, mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; }, abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.}, } @article {pmid41380668, year = {2025}, author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM}, title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.}, journal = {Cell host & microbe}, volume = {33}, number = {12}, pages = {2148-2166.e8}, doi = {10.1016/j.chom.2025.11.011}, pmid = {41380668}, issn = {1934-6069}, mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; }, abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.}, } @article {pmid41380282, year = {2025}, author = {Xu, X and Wang, J and Deng, C and Yu, X and Nie, R and Wang, S and Huang, W}, title = {Metagenomic insights into rhizosphere microbiome dynamics of Oenanthe javanica in ecological floating beds under different hydrodynamic regimes.}, journal = {Journal of contaminant hydrology}, volume = {277}, number = {}, pages = {104795}, doi = {10.1016/j.jconhyd.2025.104795}, pmid = {41380282}, issn = {1873-6009}, abstract = {Ecological floating beds (EFBs) are a cost-effective and sustainable technology that utilizes macrophyte to remove nutrients from aquatic ecosystems, where rhizosphere bacterial degradation and assimilation play a key role in nutrient removal. However, the current knowledge about how hydrodynamic regimes impact the rhizosphere bacterial community on EFB systems remains limited. Here, we investigated the effects of different hydrodynamic regimes (i.e., stagnant water, pulsed water, and flowing water conditions) on the rhizosphere bacterial community structure and function of Oenanthe javanica in an experimental EFB system based on metagenomic sequencing. We observed that bacterial community compositions on the roots of O. javanica were significantly differed across the three hydrodynamic regimes, with the highest bacterial biodiversity captured from the flowing water condition. Moreover, a total of 65 nitrogen functional genes (NFGs) were identified in the rhizosphere bacterial community, with nitrate reduction pathways dominating the nitrogen cycling processes. In contrast, totally 139 phosphorus functional genes (PFGs) were detected, primarily involved in purine metabolism, which drove the phosphorus cycling dynamics. We found the distinct nitrogen and phosphorus metabolic strategies of rhizosphere bacterial communities in response to hydrodynamic regime changes. Specifically, the relative abundances of NFGs like nasB, narl, and ansB were significantly increased under the pulsed water condition, whereas gdh_K00262 were relative abundant under the flowing condition. Moreover, pulsed water condition promoted the relative abundances of PFGs such asas phnC, phoD, and pgtP in rhizosphere bacterial communities, in contrast to the stagnant condition, which favored genes like ugpC, purK, phoH, and purA. Our study offers technical support for regulating plant degradation of pollutants to improve EFB's performance in engineering applications.}, } @article {pmid41379797, year = {2025}, author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D}, title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337322}, pmid = {41379797}, issn = {1932-6203}, mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation & purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; }, abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.

METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n = 37; 66.1%), IBD-Unclassified (n = 9; 16.1%), ulcerative proctitis (n = 7; 12.5%), and Crohn's disease (n = 3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.

RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).

CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.}, } @article {pmid41324463, year = {2025}, author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I}, title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf252}, pmid = {41324463}, issn = {1751-7370}, support = {101000213//Horizon2020/ ; ERC 866530/ERC_/European Research Council/International ; ISF 979/25//Israel Science Foundation/ ; }, mesh = {Animals ; *Rumen/microbiology/growth & development ; Cattle ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes, including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.}, } @article {pmid41270896, year = {2026}, author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M}, title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.}, journal = {Gene}, volume = {978}, number = {}, pages = {149913}, doi = {10.1016/j.gene.2025.149913}, pmid = {41270896}, issn = {1879-0038}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/pathology ; Case-Control Studies ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Pilot Projects ; Neoplasm Staging ; Adult ; Bacteria/genetics/classification ; }, abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.

METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.

RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2] = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY: aerobactin biosynthesis.

CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.}, } @article {pmid41270835, year = {2025}, author = {Gao, W and Yao, Y and Sun, Y and Pu, W and Xu, L}, title = {Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.}, journal = {Virus research}, volume = {362}, number = {}, pages = {199666}, pmid = {41270835}, issn = {1872-7492}, mesh = {Animals ; Dogs ; *Feces/virology ; China ; *Virome ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Dog Diseases/virology ; Phylogeny ; Pooled Testing ; }, abstract = {As popular companion animals, dogs present a potential risk for zoonotic viral transmission through close contact with humans. To characterize the fecal virome of dogs in Pingliang City, Gansu Province, China, we performed metatranscriptomic sequencing on 30 fecal samples pooled into three libraries, representing three distinct living environments. A total of 112,900,200 clean reads were obtained, revealing 16 viral genera spanning 15 families and highlighting a diverse viral community comprising animal viruses, bacteriophages, and plant viruses. Notably, we identified five known pathogenic viruses: canine astrovirus (3708 reads), canine dicipivirus (6578 reads), canine norovirus (16 reads), canine vesivirus (74 reads), and canine rotavirus (128 reads). Their presence suggests possible exposure events at the human-animal interface, although the infectivity and transmission risk require further experimental validation. These findings significantly expand our understanding of the canine virome and underscore the importance of "One Health" surveillance in companion animals. However, the actual zoonotic potential of the detected viruses, remains to be elucidated through further targeted investigation.}, } @article {pmid41197330, year = {2025}, author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE}, title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.}, journal = {Nutrition research (New York, N.Y.)}, volume = {144}, number = {}, pages = {1-15}, doi = {10.1016/j.nutres.2025.10.004}, pmid = {41197330}, issn = {1879-0739}, mesh = {Animals ; Female ; *Probiotics/pharmacology/therapeutic use ; Pregnancy ; *Hypertension ; *Pre-Eclampsia ; Rats ; *Fatty Acids/blood/metabolism ; *Cultured Milk Products ; Gastrointestinal Microbiome ; Blood Pressure/drug effects ; Rats, Sprague-Dawley ; Fermentation ; Esters ; *Milk ; Disease Models, Animal ; Antihypertensive Agents ; }, abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.}, } @article {pmid41192168, year = {2025}, author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA}, title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.}, journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)}, volume = {92}, number = {}, pages = {127787}, doi = {10.1016/j.jtemb.2025.127787}, pmid = {41192168}, issn = {1878-3252}, mesh = {Humans ; *Arthritis, Rheumatoid/blood/microbiology/pathology ; Male ; Female ; Middle Aged ; *Feces/microbiology ; *Trace Elements/blood ; *Minerals/blood ; *Cartilage/pathology ; *Gastrointestinal Microbiome ; Adult ; Aged ; }, abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).

MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.

RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.

CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.}, } @article {pmid41159664, year = {2025}, author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E}, title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {24}, pages = {e70289}, doi = {10.1002/mnfr.70289}, pmid = {41159664}, issn = {1613-4133}, support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; }, mesh = {*Acrolein/metabolism/urine ; Humans ; *Glycerol/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; Male ; Adult ; Female ; Biomarkers/urine ; Diet ; Acetylcysteine/urine/analogs & derivatives ; *Intestines/microbiology ; Middle Aged ; Young Adult ; }, abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.}, } @article {pmid40971838, year = {2025}, author = {Guo, X and Liang, A}, title = {Rhizosphere-derived microbiome of Ailanthus altissima drives gut microbiome composition in Lycorma delicatula (Hemiptera: Fulgoridae).}, journal = {Journal of economic entomology}, volume = {118}, number = {6}, pages = {2771-2782}, doi = {10.1093/jee/toaf217}, pmid = {40971838}, issn = {1938-291X}, support = {32470469//National Natural Science Foundation of China/ ; 32070470//National Natural Science Foundation of China/ ; 31561163003//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Rhizosphere ; *Hemiptera/microbiology ; *Ailanthus/microbiology ; Bacteria/classification/isolation & purification/genetics ; Soil Microbiology ; }, abstract = {The spotted lanternfly (SLF), Lycorma delicatula (White) (Hemiptera: Fulgoridae), a highly polyphagous invasive pest, preferentially feeds on tree-of-heaven (TOH), Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae). However, the bacterial interactions between this pest and its host plant remain poorly understood. In this study, we investigated the bacterial community composition and functional profiles in the SLF gut, TOH leaves, and TOH rhizosphere soil using amplicon and metagenomic sequencing. This study showed that the bacterial alpha-diversity differed significantly among the 3 sample types (P < 0.05). Venn analysis identified 4 shared amplicon sequence variants (ASVs) between the TOH rhizosphere soil and SLF gut, suggesting potential bacterial interactions or transfer. Further source-tracking analysis indicated that most gut bacteria originated from the rhizosphere soil. However, the dominant taxa varied across compartments: Proteobacteria dominated both the SLF gut and TOH leaves, while Acidobacteria predominated in the TOH rhizosphere soil. Network analysis revealed significant correlations between gut and rhizosphere microbes, notably Candidatus Vidania and Fastidiosipila (P < 0.05, r = 1). Functional profiling showed that the rhizosphere microbiome was enriched in nitrogen cycling and carbon fixation pathways, whereas the gut microbiome was associated with carbohydrate metabolism and nutrient assimilation. These results provide new insights into the potential roles of microbiomes in mediating plant-insect interactions and underscore the rhizosphere as a critical microbial source for SLF. Understanding these microbial connections may support the development of innovative and sustainable pest management strategies.}, } @article {pmid41379255, year = {2025}, author = {Špiljak, B and Ozretić, P and Brailo, V and Škrinjar, I and Lončar Brzak, B and Andabak Rogulj, A and Butić, I and Tambić Andrašević, A and Vidović Juras, D}, title = {Microbial dysbiosis and host-microbe interactions in proliferative verrucous leukoplakia: insights into carcinogenic potential.}, journal = {Archives of microbiology}, volume = {208}, number = {1}, pages = {65}, pmid = {41379255}, issn = {1432-072X}, mesh = {Humans ; *Dysbiosis/microbiology ; *Leukoplakia, Oral/microbiology/pathology ; Microbiota ; *Host Microbial Interactions ; Carcinogenesis ; Mouth Neoplasms/microbiology/pathology ; }, abstract = {Proliferative verrucous leukoplakia (PVL) is a rare and aggressive oral potentially malignant disorder (OPMD) characterized by multifocal keratotic plaques, progressive expansion, high recurrence, and a strong risk of malignant transformation. Although its etiology remains unclear, recent evidence emphasizes the role of the oral microbiome as a key factor in disease progression. Alterations in microbial diversity and ecological balance create a shift toward dysbiosis, supporting a chronic inflammatory microenvironment that favors epithelial transformation. Specific taxa, including Fusobacterium and Porphyromonas, have been implicated in biofilm formation, immune evasion, and modulation of epithelial signaling pathways. These interactions highlight the potential of microbial communities to drive oncogenic processes through host-microbe crosstalk. Advanced methodological approaches such as metagenomics, functional microbiome profiling, and multi-omics integration provide novel opportunities to unravel the mechanisms of dysbiosis in PVL. Beyond pathogenesis, microbiome research opens perspectives for the identification of predictive biomarkers, targeted prevention, and microbiome-based therapeutics. This review synthesizes current insights into the microbial basis of PVL and outlines future directions aimed at improving understanding of host-microbe interactions and their role in oral carcinogenesis. Relevant literature was identified through PubMed and Web of Science searches (1985-2025) using terms related to PVL, oral leukoplakia, OPMD, oral microbiome, and oral squamous cell carcinoma. In conclusion, current evidence suggests that while microbial dysbiosis is not an isolated driver, it likely synergizes with genetic, epigenetic, and immunological factors in PVL progression, offering opportunities for biomarker discovery and novel therapeutic strategies. This study also provides a potential direction for the early diagnosis of PVL and the development of microecologically targeted interventions.}, } @article {pmid41379245, year = {2025}, author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S}, title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {12}, pages = {504}, pmid = {41379245}, issn = {1573-0972}, support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; }, mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation & purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; }, abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.}, } @article {pmid41379027, year = {2025}, author = {Esvap, E and Ulgen, KO}, title = {Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations.}, journal = {Biotechnology journal}, volume = {20}, number = {12}, pages = {e70164}, doi = {10.1002/biot.70164}, pmid = {41379027}, issn = {1860-7314}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Oxidation-Reduction ; Child ; Male ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Child, Preschool ; Metagenomics ; Metabolomics ; Bacteria/metabolism/classification/genetics ; *Autistic Disorder/microbiology/metabolism ; }, abstract = {Emerging evidence suggests that disruptions in the gut microbiome may influence autism spectrum disorder (ASD) through altered microbial metabolism and gut-brain communication. However, the specific metabolic impacts of these microbial changes remain unclear. Community-scale metabolic modeling was applied to shotgun metagenomics data from children with ASD and neurotypical controls to predict secretion of host-impacting metabolites. Modeled ASD-associated communities exhibited altered predicted secretion of metabolites related to redox balance and neurotransmission, including increased 2-ketobutyrate and GABA and reduced riboflavin and inositol, with microbiota transfer therapy (MTT) shifting these profiles toward NT. Empirical fecal metabolomics data showed generally consistent directional trends with model predictions. Reductions in autism severity scores following MTT were associated with increased predicted secretion potentials for inositol and arginine. Taxonomic analysis revealed a depletion of beneficial and an enrichment of pro-inflammatory species, such as Escherichia and Flavonifractor, in ASD. Associations between microbial taxa (e.g., Bacteroides, Bifidobacterium) and neuroactive metabolites highlight microbial modulation as a promising therapeutic strategy in ASD. These results emphasize microbial metabolism as a contributor to ASD traits and a target for therapeutic intervention.}, } @article {pmid41373884, year = {2025}, author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L}, title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/ijms262311737}, pmid = {41373884}, issn = {1422-0067}, support = {LF-ST-21-500002//LEO Foundation/ ; }, mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; }, abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.}, } @article {pmid41373768, year = {2025}, author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A}, title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/ijms262311616}, pmid = {41373768}, issn = {1422-0067}, support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; }, mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation & purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation & purification ; Gastrointestinal Microbiome/genetics ; }, abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.}, } @article {pmid41370178, year = {2025}, author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS}, title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.97751}, pmid = {41370178}, issn = {2050-084X}, support = {NIHR200915//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; }, abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.}, } @article {pmid41351056, year = {2025}, author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ}, title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {253}, pmid = {41351056}, issn = {2049-2618}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; }, mesh = {*Microbiota/genetics ; *Geologic Sediments/microbiology ; *Rivers/microbiology ; North America ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Adaptation, Physiological ; Metagenomics/methods ; }, abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.

RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.

CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.}, } @article {pmid41330099, year = {2025}, author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R}, title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181101}, doi = {10.1016/j.scitotenv.2025.181101}, pmid = {41330099}, issn = {1879-1026}, mesh = {Animals ; *Oligochaeta/physiology/virology/microbiology ; *Gastrointestinal Microbiome ; Soil Pollutants/metabolism ; Inactivation, Metabolic ; RNA, Ribosomal, 16S ; Biodegradation, Environmental ; Bacteria ; Metagenome ; }, abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.}, } @article {pmid41224035, year = {2026}, author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F}, title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.}, journal = {Bioresource technology}, volume = {441}, number = {}, pages = {133630}, doi = {10.1016/j.biortech.2025.133630}, pmid = {41224035}, issn = {1873-2976}, mesh = {*Bioreactors/microbiology ; *Methane/biosynthesis ; Anaerobiosis ; *Nitrogen/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonia/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Membranes, Artificial ; Sewage/microbiology ; Biofuels ; }, abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.}, } @article {pmid40985325, year = {2025}, author = {He, J and Xiao, J and Shen, X and Zhao, K and Lei, X and Zhang, H and Sun, C and Lu, H and Shao, Y}, title = {Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {46}, pages = {e06402}, pmid = {40985325}, issn = {2198-3844}, support = {518000-523500922002//Scientific Pre-research Fund of Zhejiang University/ ; CARS-18//Agriculture Research System of China/ ; 32022081//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 31970483//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; }, mesh = {*Ecosystem ; *Microbiota/genetics ; *Agriculture/methods ; Biodiversity ; Bacteria/genetics/classification ; Fungi/genetics ; Metagenomics ; }, abstract = {Ecosystems are interconnected networks of diverse habitat types, rather than isolated patches. However, the role of the multi-habitat landscape in influencing microbial diversity remains poorly understood. This study investigates bacterial and fungal communities within a 2500-year agricultural heritage system, the Mulberry-dyke and Fish-pond (MF), which integrates various terrestrial and aquatic habitats. Using amplicon sequencing, metagenomics, metatranscriptomics, and genomic analyses, these findings reveal a significant proportion of unclassified microbial taxa, underscoring the importance of MF systems as an untapped reservoir of microbial genetic resources. Moreover, single-nucleotide-level analyses demonstrate that a multi-habitat landscape enhances microbial diversity through ecosystem-wide assembly, facilitated by cross-habitat microbial dispersal. Taxa found across multiple habitats exhibit convergence in microdiversity and adaptive genetic traits, indicating both ecological and functional mechanisms underlying their adaptability. A global analysis of public microbiome datasets furthermore confirms that regions with higher habitat heterogeneity support significantly higher taxonomic and functional diversity of microbiomes. Overall, this study sheds new light on the overlooked microbial diversity in traditional agricultural heritages and emphasizes the value of ancestral ecological wisdom underlying multi-habitat integration for ecosystem management. These insights offer valuable guidance for developing sustainable agricultural strategies, enhancing microbial diversity, and reinforcing ecosystem resilience in the face of global change.}, } @article {pmid40967406, year = {2026}, author = {Harwood, M and South, J and Dunn, AM and Stebbing, PD and Burgess, A and Bojko, J}, title = {Pathogen diversity of the non-native narrow-clawed crayfish (Pontastacus leptodactylus) in a UK water body.}, journal = {Journal of invertebrate pathology}, volume = {214}, number = {}, pages = {108458}, doi = {10.1016/j.jip.2025.108458}, pmid = {40967406}, issn = {1096-0805}, mesh = {Animals ; *Astacoidea/microbiology/parasitology/virology ; Introduced Species ; United Kingdom ; Symbiosis ; }, abstract = {Biological invasions are intrinsically linked to introducing associated symbiotic organisms, some of which can be parasitic or pathogenic. The pathogenic risk of an 'invasive parasite' (aka. exotic pathogen) stems from its potential to infect native hosts and induce behavioural change or mortality, with the pathogen potentially presenting a greater risk than the host. Conversely, parasites translocated by invasive hosts may also reduce the impact of their host, indirectly curbing the hosts impact on the invaded ecosystem. In this study, we develop a pathogen profile for the narrow-clawed crayfish, Pontastacus leptodactylus. This is a non-native species in the United Kingdom, and poses a possible risk as a sink for invasive parasites. We use histopathology, metagenomics and metratranscriptomics to outline the symbiotic diversity harboured by a P. leptodactylus population from West Yorkshire, England. We discovered several protozoan and bacterial species that appear to be putatively commensal with this invader, as well as several RNA viruses (Hepelivirales; Picornavirales; Nodaviridae, and others) that may be more pathogenic in nature. Microsporidia and Nudiviridae were absent in our population sample set, as were all metazoan obligate parasites, such as trematodes and acanthocephalans. Using the novel genomic and pathological data available to us, we have explored the evolutionary history of each symbiotic species and provided an initial assessment on the putative risk to native species.}, } @article {pmid40885432, year = {2026}, author = {Kwon, M and Kwon, SH and Jang, H and Oh, H and Sun, S and Jung, C and Kil, EJ}, title = {Landscape-scale virome analysis uncovers endemic and emerging honey bee viruses in the Silk-Road hub of Uzbekistan.}, journal = {Journal of invertebrate pathology}, volume = {214}, number = {}, pages = {108436}, doi = {10.1016/j.jip.2025.108436}, pmid = {40885432}, issn = {1096-0805}, mesh = {Animals ; Bees/virology ; *Virome ; Uzbekistan ; *RNA Viruses/isolation & purification/genetics ; Phylogeny ; *Insect Viruses/genetics/isolation & purification ; Genome, Viral ; }, abstract = {Honey bee health is increasingly threatened worldwide by a complex and evolving viral landscape; however, this aspect in Central Asia remains understudied despite the region being strategically positioned along historic and modern trade routes. In 2024, we conducted a nationwide virome survey of Apis mellifera across 32 cities in 11 regions of Uzbekistan, combining the metagenomic data of 14 pooled RNA-seq libraries with RT-PCR validation and phylogenetic analyses. High-quality sequencing yielded an average of approximately 60 million reads per pool. We recovered 30 viral species from 162 genomic sequences (131 complete sequences), including 11 honey bee-associated and 19 plant-infecting viruses. All samples harbored deformed wing virus type A (DWV-A), and co-infection with DWV-B predominated. Our findings provided the first full-length DWV-B genomes from Central Asia, revealing that it had > 97 % identity to European strains. New variants of the Sacbrood virus (partial sequence, approximately 4.7 kb) and Lake Sinai virus UZB were also detected. The chronic bee paralysis virus was sequenced in full for the first time in Uzbekistan, and varroa orthomyxovirus-1 exhibited segment-specific divergence. Additionally, we identified two novel plant viruses: Gulistan nepovirus 1 and Arpa carmo-like virus 1. Phylogenetic patterns of the identified viruses indicate that Uzbekistan serves as a genetic corridor connecting European and Asian virus populations. These findings fill critical geographical gaps, underscore the need for transboundary surveillance, and provide a genomic baseline for future diagnostics, epidemiology, and control strategies aimed at safeguarding pollinator and ecosystem health.}, } @article {pmid41369685, year = {2025}, author = {Mohammadi, R and Morovati, H and Safari, F}, title = {The human mycobiome: a critical yet understudied component of health and disease.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {12}, pages = {}, doi = {10.1099/mic.0.001631}, pmid = {41369685}, issn = {1465-2080}, mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; }, abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.}, } @article {pmid41369187, year = {2025}, author = {Calderón-Osorno, M and Rojas-Jimenez, K}, title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {12}, pages = {}, doi = {10.1099/mic.0.001632}, pmid = {41369187}, issn = {1465-2080}, mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; }, abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.}, } @article {pmid41368641, year = {2025}, author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L}, title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1696701}, pmid = {41368641}, issn = {1664-3224}, mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs & derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; }, abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.

METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.

RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/IκBα/NF-κB pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.

CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-κB signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.}, } @article {pmid41366428, year = {2025}, author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW}, title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.}, journal = {Journal of neuroinflammation}, volume = {22}, number = {1}, pages = {285}, pmid = {41366428}, issn = {1742-2094}, support = {R21 NS131689/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; }, mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; }, abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.

METHODS: C57BL6/J mice were randomized to CCI (6 m/s, 2 mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16 S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.

RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.

CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.}, } @article {pmid41338072, year = {2025}, author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S}, title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181092}, doi = {10.1016/j.scitotenv.2025.181092}, pmid = {41338072}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Microalgae/physiology ; *Soil Microbiology ; Fertilizers ; *Cyanobacteria/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Metabolomics ; Agriculture ; }, abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.}, } @article {pmid41314069, year = {2025}, author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK}, title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181062}, doi = {10.1016/j.scitotenv.2025.181062}, pmid = {41314069}, issn = {1879-1026}, mesh = {India ; Seasons ; *Microbiota ; *Railroads ; *Air Microbiology ; *Environmental Monitoring ; Cities ; Bacteria/classification ; }, abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.}, } @article {pmid41308447, year = {2025}, author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H}, title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140613}, doi = {10.1016/j.jhazmat.2025.140613}, pmid = {41308447}, issn = {1873-3336}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Drug Resistance, Microbial/drug effects/genetics ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/pharmacology ; *Anti-Inflammatory Agents/pharmacology ; Lipopolysaccharides ; Male ; }, abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.}, } @article {pmid41297255, year = {2025}, author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y}, title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140566}, doi = {10.1016/j.jhazmat.2025.140566}, pmid = {41297255}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Microbiota ; Humans ; Norway ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; }, abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.}, } @article {pmid41297254, year = {2025}, author = {Hatwar, N and Qureshi, A}, title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140589}, doi = {10.1016/j.jhazmat.2025.140589}, pmid = {41297254}, issn = {1873-3336}, mesh = {*Polyvinyl Chloride/metabolism ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/metabolism/genetics/isolation & purification ; *Microbial Consortia ; Solid Waste ; Soil Microbiology ; Refuse Disposal ; }, abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.}, } @article {pmid41273973, year = {2025}, author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z}, title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140564}, doi = {10.1016/j.jhazmat.2025.140564}, pmid = {41273973}, issn = {1873-3336}, mesh = {*Rivers/virology ; China ; *Bacteriophages/genetics/physiology ; *Ecosystem ; Fresh Water/virology ; Virome ; Geologic Sediments ; }, abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.}, } @article {pmid41237940, year = {2026}, author = {Borroni, D and Lo Monaco, F and Ferraro, S and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C}, title = {Ocular surface microbiota in primary open angle glaucoma.}, journal = {Experimental eye research}, volume = {262}, number = {}, pages = {110734}, doi = {10.1016/j.exer.2025.110734}, pmid = {41237940}, issn = {1096-0007}, mesh = {Humans ; *Glaucoma, Open-Angle/microbiology/drug therapy ; Cross-Sectional Studies ; Male ; Female ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; *Bacteria/genetics/isolation & purification ; Intraocular Pressure/physiology ; DNA, Bacterial/genetics ; *Conjunctiva/microbiology ; *Dysbiosis/microbiology ; }, abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1 × 10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.}, } @article {pmid41237630, year = {2025}, author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L}, title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140469}, doi = {10.1016/j.jhazmat.2025.140469}, pmid = {41237630}, issn = {1873-3336}, mesh = {*Wetlands ; *Soil Microbiology ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics ; Metagenome ; Microbiota ; }, abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.}, } @article {pmid41237622, year = {2025}, author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J}, title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140425}, doi = {10.1016/j.jhazmat.2025.140425}, pmid = {41237622}, issn = {1873-3336}, mesh = {*Pisum sativum/microbiology/growth & development/drug effects/metabolism ; *Rhizosphere ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Metabolomics ; *Polyethylene/toxicity ; Soil Microbiology ; *Microbiota/drug effects ; *Microplastics/toxicity ; *Soil Pollutants/toxicity ; Genes, Bacterial ; Bacteria/genetics/drug effects ; }, abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.}, } @article {pmid41223471, year = {2025}, author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X}, title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140406}, doi = {10.1016/j.jhazmat.2025.140406}, pmid = {41223471}, issn = {1873-3336}, mesh = {*Sulfamethoxazole/pharmacology/toxicity ; *Microalgae/drug effects/genetics/physiology/metabolism ; *Water Pollutants, Chemical/toxicity ; Adaptation, Physiological ; *Bacteria/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbial Consortia/drug effects ; Reactive Oxygen Species/metabolism ; Photosynthesis/drug effects ; }, abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.}, } @article {pmid41222145, year = {2025}, author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE}, title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.}, journal = {mBio}, volume = {16}, number = {12}, pages = {e0234125}, doi = {10.1128/mbio.02341-25}, pmid = {41222145}, issn = {2150-7511}, support = {R35 GM151045/GM/NIGMS NIH HHS/United States ; T32 GM156692/GM/NIGMS NIH HHS/United States ; R01 GM147178/GM/NIGMS NIH HHS/United States ; R00 AI147165/AI/NIAID NIH HHS/United States ; T32 DK120509/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/physiology/isolation & purification/genetics ; *Bacteroides/virology/genetics ; Germ-Free Life ; }, abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.

IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.}, } @article {pmid41192191, year = {2026}, author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB}, title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {57}, number = {}, pages = {101666}, doi = {10.1016/j.cbd.2025.101666}, pmid = {41192191}, issn = {1878-0407}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Metabolomics ; *Metagenomics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/classification/metabolism ; Anti-Bacterial Agents/pharmacology ; *Fishes/microbiology/metabolism ; Metagenome ; }, abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.}, } @article {pmid41192179, year = {2025}, author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC}, title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140319}, doi = {10.1016/j.jhazmat.2025.140319}, pmid = {41192179}, issn = {1873-3336}, mesh = {*Diethylhexyl Phthalate/toxicity/metabolism ; Biodegradation, Environmental ; *Plasticizers/toxicity/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; *Water Pollutants, Chemical/metabolism/toxicity ; Anaerobiosis ; Bacteria/metabolism/genetics ; *Ammonium Compounds/metabolism ; }, abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.}, } @article {pmid41175632, year = {2026}, author = {Patel, AB and Jain, KR and Gupta, V and Lal, R and Madamwar, D}, title = {Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.}, journal = {Marine environmental research}, volume = {213}, number = {}, pages = {107665}, doi = {10.1016/j.marenvres.2025.107665}, pmid = {41175632}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Ships ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Bacteria/classification ; India ; Metals, Heavy/analysis ; Metagenome ; Biodiversity ; }, abstract = {Coastal ecosystems, like many others on the planet, face chronic threats from anthropogenic activities. The Alang-Sosiya Ship Breaking Yard (ASSBY) located near Bhavnagar in Gujarat, India, represents one such ecosystem impacted by decades of ship-breaking activities. This study aimed to assess the differences in microbial community composition between polluted coastal samples and pristine samples through high-throughput sequencing. Additionally, microbial co-occurrence networks and genes related to antibiotic and heavy metal resistance were predicted using metagenome mining. The analysis confirmed elevated heavy metal concentrations, particularly iron, in polluted samples. In non-polluted sites, alpha diversity indices showed a high microbial diversity compared to polluted sites. The bacterial communities from Deltaproteobacteria at non-polluted sites noticeably shifted to Gammaproteobacteria at polluted sites. Unclassified reads constituted a significant portion of the bacterial diversity. LEfSe (Linear discriminant analysis Effect Size) analysis identified potential bacterial biomarkers, including Pseudomonas, Halomonas and Rhodovulum, which were differentially abundant at polluted sites and may play roles in the biodegradation of xenobiotic compounds. Moreover, Co-occurrence network analysis validated these bacterial biomarkers from polluted sites and revealed their habitat-specific nature. Polluted metagenomes were enriched with genes related to aromatic compound degradation and stress responses, particularly genes for heavy metal and antibiotic resistance. These findings suggest that chronic pollution from ship-breaking activities has led to a shift in microbial communities, leading to an increased presence of resistance mechanisms in the polluted coastal environment to adapt to prolonged heavy pollution.}, } @article {pmid41086610, year = {2026}, author = {Li, H and Gao, H and Chen, S and Li, X and Zhou, J}, title = {Intensive mariculture shifts microbial communities and life-history strategies in the semi-enclosed bay: Case study in Sansha Bay, China.}, journal = {Marine environmental research}, volume = {213}, number = {}, pages = {107607}, doi = {10.1016/j.marenvres.2025.107607}, pmid = {41086610}, issn = {1879-0291}, mesh = {China ; *Bays/microbiology ; *Microbiota ; *Aquaculture ; Eutrophication ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; Animals ; }, abstract = {Coastal bays often experience significant disturbances from various mariculture activities, frequently leading to severe eutrophication. Yet, the ecological consequences of nutrient inputs derived from mariculture on bay-associated microbial communities remain insufficiently understood. Sansha Bay, known as the world's largest cage mariculture site for Larimichthys crocea, represents a characteristic semi-enclosed bay commonly utilized for studying the environmental impacts of intensive mariculture. In this study, we compared the highly eutrophic Sansha Bay with the relatively undisturbed natural East China Sea to investigate how intensive mariculture influences the bay microbial biosphere, focusing on community composition, assembly mechanisms, functional profiles, and life-history strategies. Amplicon sequencing and metagenomic analyses showed that Sansha Bay had a greater proportion of fast-growing microorganisms, nitrogen and carbon cycling microbes, and antibiotic-resistant bacteria. Null model analysis indicated that while natural coastal microbial assemblages were predominantly shaped by stochastic processes, deterministic selection became increasingly prominent as mariculture activities intensified. Correspondingly, microbial life-history traits, including 16S rRNA gene copy number, codon usage bias, predicted maximum growth rates, genome size, guanine-cytosine content, transposase abundance, and niche breadth, were consistently elevated in the eutrophic bay. These results suggest that eutrophication associated with mariculture drives a shift in life-history strategies from oligotrophs (K-strategists) to copiotrophs (r-strategists). Collectively, this study yields novel mechanistic understanding of how intensive mariculture reshapes microbial community structures, laying the groundwork for forecasting changes in coastal ecosystems subjected to ongoing human disturbances.}, } @article {pmid40915974, year = {2026}, author = {Ribeiro, MC and Colombo, APV and de Oliveira, AM and Lourenço, TGB and Honório, HM and de Freitas, EC and Messora, MR and Furlaneto, FAC}, title = {The Interplay Between Lifestyle and Oral/Faecal Microbial Profiles Among Periodontal Disease Patients: A Cross-Sectional Study.}, journal = {Journal of clinical periodontology}, volume = {53}, number = {1}, pages = {82-97}, doi = {10.1111/jcpe.70029}, pmid = {40915974}, issn = {1600-051X}, mesh = {Humans ; Cross-Sectional Studies ; *Feces/microbiology ; Male ; Female ; Middle Aged ; *Life Style ; Adult ; *Periodontal Diseases/microbiology ; *Mouth/microbiology ; *Microbiota ; *Periodontitis/microbiology ; Biofilms ; Gingivitis/microbiology ; Aged ; RNA, Ribosomal, 16S ; Diet ; }, abstract = {AIM: To characterise periodontal and faecal microbiomes of individuals with periodontal health (PH) and diseases, and evaluate associations with periodontal, sociodemographic, anthropometric, nutritional and lifestyle factors.

MATERIALS AND METHODS: Dental biofilm and faecal samples from individuals (n = 24/group) with PH, gingivitis (GG) and periodontitis (PE) were sequenced (16S rRNA). Anthropometric data and questionnaires on demographics, lifestyle, diet and intestinal habits were collected. Data were statistically analysed (p < 0.05).

RESULTS: GG and PE groups showed higher age, BMI, waist/abdominal circumferences and trans-fat intake and lower selenium and vitamin E intake compared to PH. Individuals with PE had higher hip circumference and lower income, education and intake of iron as well as vitamins A and B9. PE microbiomes (oral and faecal) showed distinct compositions, with the highest number of unique oral species. Faecal richness was lower in PE and GG compared to PH. Specific microbial taxa correlated with periodontal status and host factors.

CONCLUSION: Periodontal and faecal microbiomes vary across periodontal conditions. Discriminant analysis classified 77% of individuals by periodontal status, with key markers for PE including older age, poor dietary quality and distinct microbial oral and faecal signatures. These findings highlight the role of clinical, dietary and microbial factors in periodontal disease profiling.}, } @article {pmid41365917, year = {2025}, author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D}, title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {227}, pmid = {41365917}, issn = {2055-5008}, support = {314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; }, mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; }, abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.}, } @article {pmid41365804, year = {2025}, author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S}, title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70249}, doi = {10.1111/1758-2229.70249}, pmid = {41365804}, issn = {1758-2229}, support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; }, abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.}, } @article {pmid41361579, year = {2025}, author = {Anunobi, OO and Abiola, RB and Ogah, CF}, title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {1}, pages = {6}, pmid = {41361579}, issn = {1572-9699}, mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation & purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.}, } @article {pmid41360540, year = {2026}, author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J}, title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {223}, number = {Pt 2}, pages = {117842}, doi = {10.1016/j.foodres.2025.117842}, pmid = {41360540}, issn = {1873-7145}, mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; }, abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.}, } @article {pmid41354993, year = {2025}, author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D}, title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43425}, pmid = {41354993}, issn = {2045-2322}, support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Ursidae/microbiology ; *Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use ; *Antibiotic Prophylaxis ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Cefotaxime/pharmacology/administration & dosage ; Feces/microbiology ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/classification ; }, abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.}, } @article {pmid41093042, year = {2025}, author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P}, title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.}, journal = {Plasmid}, volume = {134}, number = {}, pages = {102761}, doi = {10.1016/j.plasmid.2025.102761}, pmid = {41093042}, issn = {1095-9890}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Plasmids/genetics ; Infant ; Feces/microbiology ; Infant, Newborn ; Bacteroides/genetics ; Longitudinal Studies ; Female ; Computational Biology/methods ; Male ; Clostridium/genetics ; }, abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.}, } @article {pmid40972220, year = {2026}, author = {Saha, S and Mondal, A and Bag, S and Ghosh, S and Mandal, AH and Saha, NC and Chatterjee, S and Sopjani, M and Multisanti, CR and Faggio, C}, title = {Are biopesticides really safe? Impacts on gut microbiota and intestinal health in freshwater fish.}, journal = {Journal of contaminant hydrology}, volume = {276}, number = {}, pages = {104727}, doi = {10.1016/j.jconhyd.2025.104727}, pmid = {40972220}, issn = {1873-6009}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fishes/microbiology ; Fresh Water ; *Biological Control Agents/toxicity ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; *Intestines/drug effects ; Pesticides/toxicity ; }, abstract = {The growing use of biopesticides as eco-friendly alternatives to chemical pesticides is reshaping pest control in agriculture and aquaculture. However, their potential effects on non-target aquatic species, particularly freshwater fish, remain underexplored. This review investigates how different biopesticides, such as microbial agents, biochemical compounds, and plant-incorporated protectants, affect the gut microbiota and intestinal health of freshwater fish. The gut microbiome plays a vital role in digestion, nutrient absorption, immunity, and overall fish health. Biopesticide exposure may disrupt microbial balance, leading to reduced diversity, changes in community composition, inflammation, and dysbiosis. These alterations can impair digestive efficiency, immune function, growth, and reproduction. Promising mitigation strategies include the use of probiotics, prebiotics, symbiotics, insect-based feeds and other non-bacterial dietary interventions to restore gut homeostasis and improve fish resilience. In addition, advanced techniques like metagenomics and metabolomics are enhancing our understanding of host-microbiome interactions under biopesticide exposure. This review emphasizes the importance of including gut microbiota health in environmental risk assessments for biopesticide use in aquaculture. Future studies should adopt a multidisciplinary approach combining toxicology, microbiology, nutrition, and environmental science to develop species-specific, long-term strategies that safeguard fish health in increasingly pesticide-influenced aquatic environments.}, } @article {pmid40407188, year = {2025}, author = {Batarseh, TN and Koskella, B}, title = {Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf107}, pmid = {40407188}, issn = {1751-7370}, support = {//San Francisco Chan-Zuckerberg Biohub. BK is the San Francisco Chan-Zuckerberg Biohub Investigator/ ; #2209111//National Science Foundation Postdoctoral Research Fellowship in Biology/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification ; *Biological Evolution ; Genetic Variation ; Genome, Bacterial ; }, abstract = {Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptive process in response to selection. In contrast, ecological dynamics describe changes in population densities, species distributions, species interactions, and/or relative abundances within communities, all of which can also be the result of either stochastic or deterministic processes. Although the distinction between these patterns has long held for plants and animals, microbial community dynamics can blur the line between ecological and evolutionary processes, especially as they can occur on very similar timescales. Despite the importance of differentiating changes occurring within a population or strain from those occurring among populations, many common methodologies used to study microbiomes are not able to differentiate among them. In this review, we summarize the forces known to generate genetic diversity in bacterial genomes and describe the approaches used to study bacterial evolution from simple to more complex systems. We then explore how current methodologies and conceptual understanding can be applied to both understand and differentiate between the ecological and evolutionary processes in microbial communities. By highlighting lessons from longitudinal microbiome studies and experimental evolution, we explore the unique opportunities afforded by newer sequencing approaches and better sequencing resolution. Throughout, we identify the unique and outstanding challenges in studying these processes in microbiome systems and emphasize the great benefits in doing so to move forward our ability to better predict and manipulate microbiomes.}, } @article {pmid41358671, year = {2025}, author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE}, title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2587966}, doi = {10.1080/19490976.2025.2587966}, pmid = {41358671}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & purification ; Biodiversity ; }, abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.}, } @article {pmid41355553, year = {2025}, author = {Kim, MJ and Park, JH and Eom, YB}, title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70197}, doi = {10.1002/mbo3.70197}, pmid = {41355553}, issn = {2045-8827}, support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; }, mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation & purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; }, abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.}, } @article {pmid41355481, year = {2025}, author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD}, title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70121}, doi = {10.1002/mbo3.70121}, pmid = {41355481}, issn = {2045-8827}, support = {//This study was supported by Ministerio de Ciencia e Innovación, Spain (grant PID2021-124174OB-I00)./ ; }, mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; }, abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.}, } @article {pmid41353034, year = {2025}, author = {McCone, N and Hosokawa, M}, title = {Recovering genomes from uncultured fungi with single-cell genomics.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2025.11.004}, pmid = {41353034}, issn = {1347-4421}, abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.}, } @article {pmid41270588, year = {2025}, author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK}, title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.}, journal = {The Science of the total environment}, volume = {1008}, number = {}, pages = {180981}, doi = {10.1016/j.scitotenv.2025.180981}, pmid = {41270588}, issn = {1879-1026}, mesh = {India ; *Air Microbiology ; *Bacteria/pathogenicity/classification ; *Environmental Monitoring ; *Air Pollutants/analysis ; Biodiversity ; *Microbiota ; Himalayas ; }, abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.}, } @article {pmid41260397, year = {2026}, author = {Abbasi, E}, title = {Metagenomic surveillance of emerging viruses in mosquito populations from high-risk regions of Iran.}, journal = {Journal of virological methods}, volume = {340}, number = {}, pages = {115301}, doi = {10.1016/j.jviromet.2025.115301}, pmid = {41260397}, issn = {1879-0984}, mesh = {Animals ; Iran/epidemiology ; *Culicidae/virology ; *Metagenomics ; Phylogeny ; *Arboviruses/genetics/classification/isolation & purification ; *Mosquito Vectors/virology ; *Virome ; High-Throughput Nucleotide Sequencing ; Epidemiological Monitoring ; Computational Biology ; RNA, Viral/genetics ; }, abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.

METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.

RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.

CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.}, } @article {pmid41077176, year = {2025}, author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R}, title = {Microbiome signatures and their role in uveitis: Pathogenesis, diagnostics, and therapeutic perspectives.}, journal = {Progress in retinal and eye research}, volume = {109}, number = {}, pages = {101409}, doi = {10.1016/j.preteyeres.2025.101409}, pmid = {41077176}, issn = {1873-1635}, mesh = {Humans ; *Uveitis/microbiology/diagnosis/therapy/immunology ; Animals ; Dysbiosis ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; }, abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.}, } @article {pmid41351142, year = {2025}, author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A}, title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-025-12365-4}, pmid = {41351142}, issn = {1471-2164}, abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.

RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.

CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.}, } @article {pmid41350543, year = {2025}, author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL}, title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43215}, pmid = {41350543}, issn = {2045-2322}, support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; }, mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; }, abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.}, } @article {pmid41297753, year = {2026}, author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S}, title = {Phosphate-iron modified Enteromorpha Prolifera hydrochar enhances dry anaerobic digestion of food waste: Synergistic mechanisms of electron transfer network, microbial consortia remodeling, and metagenomic insights.}, journal = {Environmental research}, volume = {289}, number = {}, pages = {123385}, doi = {10.1016/j.envres.2025.123385}, pmid = {41297753}, issn = {1096-0953}, mesh = {Anaerobiosis ; Iron/chemistry ; *Microbial Consortia ; Phosphates/chemistry ; *Ulva ; *Refuse Disposal/methods ; Electron Transport ; Metagenomics ; Solid Waste ; Food Loss and Waste ; Edible Seaweeds ; }, abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6 % improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32 %. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9 %) and hydrogenotrophic methanogens Methanoculleus (+17.7 %); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255 %), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.}, } @article {pmid41275679, year = {2026}, author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J}, title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124956}, doi = {10.1016/j.watres.2025.124956}, pmid = {41275679}, issn = {1879-2448}, mesh = {*Biodegradation, Environmental ; *Mining ; *Microbial Consortia ; Bioreactors ; }, abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.}, } @article {pmid41218435, year = {2026}, author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y}, title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124889}, doi = {10.1016/j.watres.2025.124889}, pmid = {41218435}, issn = {1879-2448}, mesh = {RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota ; Metagenomics ; Ecosystem ; Nitrates ; Bacteria/genetics ; }, abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.}, } @article {pmid40912476, year = {2025}, author = {Lu, Z and Petersen, C and Dai, R and Reyna, ME and Ahmadiankalati, M and Sifuentes, E and Dai, DLY and Hoskinson, C and Del Bel, KL and Miliku, K and Moraes, TJ and Mandhane, PJ and Becker, AB and Azad, MB and Simons, E and Lou, W and Ambalavanan, A and Duan, Q and Turvey, SE and Subbarao, P}, title = {Early-preschool wheeze trajectories are predominantly nonallergic with distinct biologic and microbiome traits.}, journal = {The Journal of allergy and clinical immunology}, volume = {156}, number = {6}, pages = {1556-1572}, doi = {10.1016/j.jaci.2025.07.034}, pmid = {40912476}, issn = {1097-6825}, mesh = {Humans ; *Respiratory Sounds/immunology ; Infant ; Female ; Male ; Child, Preschool ; *Asthma/diagnosis/epidemiology/microbiology/immunology ; Phenotype ; *Microbiota ; Cohort Studies ; Hypersensitivity ; }, abstract = {BACKGROUND: Disentangling preschool wheezing heterogeneity in terms of clinical traits, temporal patterns, and collective health care burden is critical for precise and effective interventions.

OBJECTIVE: We aimed to collectively define contributions and distinct characteristics of respiratory phenotypes based on longitudinal wheeze and atopic sensitization patterns in the first 5 years of life.

METHODS: Group-based trajectory analysis was performed in the CHILD Cohort Study to identify distinct wheeze and allergic sensitization trajectories. Trajectories were evaluated for associated risk factors, health care utilization, biologic determinants, and clinical outcomes. Stool samples for shotgun metagenomic sequencing profiles of infant microbiomes collected at ages 3 months and 1 year were assessed for phenotype-specific biomarkers.

RESULTS: A total of 6 distinct respiratory phenotypes were identified on the basis of samples from 2902 children; the phenotypes differed by temporal wheeze and allergic sensitization patterns. Although allergic wheeze phenotypes (found in 11.6% of participants) carried the highest risk of asthma diagnosis, the more common nonallergic phenotypes (in 88.3% of participants) contributed to the majority of 5-year asthma diagnoses (61.4% of diagnoses). Most importantly, nonallergic phenotypes accounted for more than two-thirds of health care utilization in this age group. Phenotypes differed by lung function, blood eosinophil counts, allergic comorbidities, and weight-for-age z score. Moreover, microbiome profiles developed from 1439 infants revealed that largely nonoverlapping microbial signatures at age 1 year are associated with each phenotype.

CONCLUSION: We identified novel early-childhood respiratory phenotypes to disentangle nonoverlapping paths to preschool wheezing. Our findings highlight the continued clinical relevance of nonatopic wheeze phenotypes, which remain undertreated despite accounting for a substantial proportion of health care utilization and asthma diagnoses.}, } @article {pmid40691354, year = {2026}, author = {Roux, S and Coclet, C}, title = {Viromics approaches for the study of viral diversity and ecology in microbiomes.}, journal = {Nature reviews. Genetics}, volume = {27}, number = {1}, pages = {32-46}, pmid = {40691354}, issn = {1471-0064}, mesh = {*Microbiota/genetics ; *Viruses/genetics/classification ; *Virome/genetics ; Humans ; Metagenomics/methods ; Ecosystem ; Genetic Variation ; Biodiversity ; Animals ; Genome, Viral ; }, abstract = {Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.}, } @article {pmid41350329, year = {2025}, author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T}, title = {Differences in prokaryotic and viral community between rumen and feces.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43232}, pmid = {41350329}, issn = {2045-2322}, mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; }, abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.}, } @article {pmid41348832, year = {2025}, author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A}, title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337760}, doi = {10.1371/journal.pone.0337760}, pmid = {41348832}, issn = {1932-6203}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.}, } @article {pmid41348596, year = {2025}, author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA}, title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, doi = {10.1093/bib/bbaf638}, pmid = {41348596}, issn = {1477-4054}, support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; }, mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; }, abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.}, } @article {pmid41348453, year = {2025}, author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z}, title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001493}, pmid = {41348453}, issn = {2057-5858}, mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; }, abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.}, } @article {pmid41348443, year = {2025}, author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM}, title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001574}, pmid = {41348443}, issn = {2057-5858}, mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; }, abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.}, } @article {pmid41346331, year = {2025}, author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M}, title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.}, journal = {Journal of food science}, volume = {90}, number = {12}, pages = {e70751}, doi = {10.1111/1750-3841.70751}, pmid = {41346331}, issn = {1750-3841}, support = {BT/PR46349/AAQ/3/1063/2022// Department of Biotechnology/ ; // Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; }, abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.}, } @article {pmid41346299, year = {2025}, author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z}, title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11806}, pmid = {41346299}, issn = {1520-5851}, abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.}, } @article {pmid41345123, year = {2025}, author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM}, title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1913}, pmid = {41345123}, issn = {2052-4463}, support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; }, mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; }, abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.}, } @article {pmid41253025, year = {2025}, author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP}, title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {149}, number = {}, pages = {157550}, doi = {10.1016/j.phymed.2025.157550}, pmid = {41253025}, issn = {1618-095X}, mesh = {*Rheum/chemistry/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/metabolism ; *Diarrhea/chemically induced/therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; Male ; *Lactobacillus ; Wine ; Mice ; }, abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.

PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.

METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-κB), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.

RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-α, IL-17, and IFN-γ), inhibit the expression of TLR4/NF-κB, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.

CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-κB and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.}, } @article {pmid40300566, year = {2025}, author = {Komijani, M and Mahdi, ES and Komijani, M and Alaghmand, A}, title = {Metagenomics Study Suggests the Role of Vitamins and Gut Microbiome in Autism Spectrum Disorder.}, journal = {Digestion}, volume = {106}, number = {6}, pages = {515-529}, doi = {10.1159/000545483}, pmid = {40300566}, issn = {1421-9867}, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/blood ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenomics ; Male ; Feces/microbiology ; Female ; Folic Acid/blood ; Case-Control Studies ; Child, Preschool ; Child ; *Vitamin B 12/blood ; RNA, Ribosomal, 16S/genetics ; *Cholecalciferol/blood ; *Vitamins/blood ; }, abstract = {INTRODUCTION: Autism is a neurological disability that often appears after the age of three in children, also known as an autism spectrum disorder (ASD). Several studies have examined the influence of some environmental factors, and many parameters related to the behavior of autistic patients have been measured in order to find ways to reduce ASD. This study investigates the relationship between ASD and serum levels of vitamin D3, B12, folic acid, and the gut microbiome.

METHODS: The serum levels of vitamin D3, B12, and folic acid in ASD patients were measured by the ELISA method and compared to healthy groups. DNA was extracted from stool samples of ASD patients and the control group, and then the gut microbiome was investigated via a metagenomics approach. Metagenomics sequencing was performed to analyze the 16S rRNA gene sequencing for phylum and sub phylum level microbiome.

RESULT: The result showed no significant change in the VitD3 and folate levels of ASD patients compared to the control group (p = 0.157 and p = 0.0505, respectively). There was a significant difference in the VitB12 level between control healthy individuals and ASD patients, in which the serum VitB12 concentration was significantly lower than the control group (p = 0.0001). Our results regarding gut metagenomics showed that the abundance of the Actinobacteria by the phylum level was significantly higher in the ASD patients compared to the control group (p = 0.0013). The abundance of the Firmicutes by the phylum level was significantly lower in the ASD patients compared to the control group (p = 0.0016). The abundance of Bifidobacteriaceae, and Ruminococcaceae by the family level was significantly higher in the ASD patients compared to the control group (p = 0.0004 and p = 0.0489, respectively). Our results indicated less species richness in the ASD patients compared to the control group.

CONCLUSION: Patients with ASD have lower serum levels of vitamin B12 and different gut microbiome compared to healthy controls. Low vitamin B12 levels and altered gut microbiome are significantly associated with ASD in this study. However, further research is needed to determine whether these factors could serve as predictors of severe outcomes in ASD.}, } @article {pmid39827989, year = {2025}, author = {Cheng, CK and Ye, L and Wang, Y and Wang, YL and Xia, Y and Wong, SH and Chen, S and Huang, Y}, title = {Exercised gut microbiota improves vascular and metabolic abnormalities in sedentary diabetic mice through gut‒vascular connection.}, journal = {Journal of sport and health science}, volume = {14}, number = {}, pages = {101026}, pmid = {39827989}, issn = {2213-2961}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Physical Conditioning, Animal/physiology ; *Fecal Microbiota Transplantation ; *Diabetes Mellitus, Type 2/therapy/metabolism/physiopathology ; Mice ; Male ; Sedentary Behavior ; Oxidative Stress ; Mice, Inbred C57BL ; Endoplasmic Reticulum Stress ; MicroRNAs/metabolism ; Endothelium, Vascular ; Receptors, Leptin ; }, abstract = {BACKGROUND: Exercise elicits cardiometabolic benefits, reducing the risks of cardiovascular diseases and type 2 diabetes. This study aimed to investigate the vascular and metabolic effects of gut microbiota from exercise-trained donors on sedentary mice with type 2 diabetes and the potential mechanism.

METHODS: Leptin receptor-deficient diabetic (db/db) and nondiabetic (db/m[+]) mice underwent running treadmill exercise for 8 weeks, during which fecal microbiota transplantation (FMT) was parallelly performed from exercise-trained to sedentary diabetic (db/db) mice. Endothelial function, glucose homeostasis, physical performance, and vascular signaling of recipient mice were assessed. Vascular and intestinal stresses, including inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, were investigated. RNA sequencing analysis on mouse aortic and intestinal tissues was performed. Gut microbiota profiles of recipient mice were evaluated by metagenomic sequencing.

RESULTS: Chronic exercise improved vascular and metabolic abnormalities in donor mice. Likewise, FMT from exercised donors retarded body weight gain and slightly improved grip strength and rotarod performance in recipient mice. Exercise-associated FMT enhanced endothelial function in different arteries, suppressed vascular and intestinal stresses, and improved glucose homeostasis in recipient mice, with noted microRNA-181b upregulation in aortas and intestines. Altered gut microbiota profiles and gut-derived factors (e.g., short-chain fatty acids and glucagon-like peptide-1) as well as improved intestinal integrity shall contribute to the cardiometabolic benefits, implying a gut‒vascular connection.

CONCLUSION: This proof-of-concept study indicates that exercised microbiota confers cardiometabolic benefits on sedentary db/db mice, extending the beneficial mechanism of exercise through gut‒vascular communication. The findings open up new therapeutic opportunities for cardiometabolic diseases and shed light on the development of exercise mimetics by targeting the gut microbiota.}, } @article {pmid41345120, year = {2025}, author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A}, title = {The Basque Coast Estuarine Sediment Gene Catalogue.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1909}, pmid = {41345120}, issn = {2052-4463}, support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; }, abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.}, } @article {pmid41345102, year = {2025}, author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M}, title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10051}, pmid = {41345102}, issn = {2041-1723}, support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; }, mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; }, abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.}, } @article {pmid41344778, year = {2026}, author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S}, title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104986}, doi = {10.1016/j.fm.2025.104986}, pmid = {41344778}, issn = {1095-9998}, mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation & purification ; Bacteriophages/genetics/classification/isolation & purification ; *Microbiota ; Food Microbiology ; }, abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.}, } @article {pmid41340567, year = {2025}, author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M}, title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593050}, doi = {10.1080/19490976.2025.2593050}, pmid = {41340567}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Vegans ; Metagenome ; Multiomics ; }, abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.}, } @article {pmid41340070, year = {2025}, author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM}, title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {249}, pmid = {41340070}, issn = {2049-2618}, mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.

RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.

CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.}, } @article {pmid41339710, year = {2025}, author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL}, title = {Microbial model communities exhibit widespread metabolic interdependencies.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-025-09306-y}, pmid = {41339710}, issn = {2399-3642}, support = {grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; }, abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.}, } @article {pmid41093108, year = {2025}, author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V}, title = {Inverse Association between Serum Vitamin B12 Level and Abundance of Potential B12-Producing Gut Microbes in Indian Children.}, journal = {The Journal of nutrition}, volume = {155}, number = {12}, pages = {4284-4295}, doi = {10.1016/j.tjnut.2025.10.021}, pmid = {41093108}, issn = {1541-6100}, mesh = {Humans ; *Vitamin B 12/blood/biosynthesis ; *Gastrointestinal Microbiome ; India ; *Vitamin B 12 Deficiency/blood/microbiology/epidemiology ; Male ; Female ; Feces/microbiology ; Child ; Child, Preschool ; Bacteria/classification/metabolism/genetics ; }, abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B vitamins, which are used by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.

OBJECTIVES: This study tested whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking vitamin B12 as a case example.

METHODS: Fecal samples were collected from non-deficient (serum vitamin B12 level > 210 pg/mL; n = 29) and vitamin B12 deficient (serum vitamin B12 level < 210 pg/mL; n = 30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential vitamin B12 producers were compared, and their association with serum vitamin B12 level was established.

RESULTS: A comparison of within-sample diversity between the two groups did not show any difference; however, between-sample diversity was significantly less in the vitamin B12-deficient group. Differential abundance testing also showed different microbiome structure in the vitamin B12-deficient group, where a higher abundance of vitamin B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known vitamin B12 producers was observed. Potential vitamin B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum vitamin B12 levels.

CONCLUSIONS: A higher abundance of potential vitamin B12 producers in the deficient group suggest an adaptive mechanism by the gut microbiome to meet the community's vitamin B12 requirements, by selectively promoting the growth of vitamin B12 producers, but causality remains to be proved.}, } @article {pmid41025564, year = {2025}, author = {Zeng, S and Wang, H and Zhang, L and Li, S and Yuan, Y and Tian, M and Qu, Y and Ying, J and Zhou, M and Hu, Y and Huang, J and Zou, R and Zhao, F and Su, X and Liu, Q and He, Y and Feng, J and Huang, W and Luo, Y and Zhou, Z and Shen, W and Mu, D and Wang, S}, title = {The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {45}, pages = {e05154}, doi = {10.1002/advs.202505154}, pmid = {41025564}, issn = {2198-3844}, support = {2021YFC2701704//National Key Research and Development Program/ ; 2021YFC2701700//National Key Research and Development Program/ ; 82402025//National Natural Science Foundation of China/ ; 82241036//National Natural Science Foundation of China/ ; 82271749//National Natural Science Foundation of China/ ; 82371717//National Natural Science Foundation of China/ ; 82201905//National Natural Science Foundation of China/ ; 82571980//National Natural Science Foundation of China/ ; 82530056//National Natural Science Foundation of China/ ; 2025ZNSFSC1677//Department of Science and Technology of Sichuan Province/ ; SCU2023D006//Fundamental Research Funds for the Central University/ ; SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; }, mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; Female ; Male ; Metagenome/genetics ; Machine Learning ; }, abstract = {The accelerating threat from antimicrobial resistance (AMR) has become a global health issue. The properties of AMR in the gut microbiome of preterm infants and its clinical relevance with necrotizing enterocolitis (NEC) remain unknown. In-depth integrative analyses of 5,684 gut metagenomes are performed to build an AMR genes (ARGs) landscape. A subset of 107 preterm infants who developed NEC is sampled to examine the trajectory and predictive potential of ARGs preceding NEC onset. The variation and core set of ARGs, their higher burden and diversity, and potential ARGs-enriched gut bacteria in preterm infants compared to full-term infants are comprehensively discovered, reflecting a strain shift in genomic functions. Moreover, the gut resistome converged over 9 days before NEC onset is observed, which is driven by 24 ARGs. Machine learning analysis reveals potential usage of the gut resistome as an indicator for predicting NEC onset in an external validation preterm birth cohort (the area under the receiver operating characteristic curve, AU-ROC = 0.823), which is significantly higher than that based on the bacterial species (AU-ROC = 0.727). Overall, the findings can be referenced to mitigate the burden and spread of ARGs, and specific ARGs have potential for disease risk stratification to improve clinical management.}, } @article {pmid41015376, year = {2025}, author = {Zhao, JX and Wang, XY and Zhang, X and Tang, LY and Xie, SC and Lv, YH and Zheng, Z and Gao, YQ and Jiang, J and Zhang, XX and Ma, H}, title = {Toxoplasma gondii alters gut microbiota and systemic metabolism in cats: A multi-omics approach.}, journal = {Veterinary journal (London, England : 1997)}, volume = {314}, number = {}, pages = {106455}, doi = {10.1016/j.tvjl.2025.106455}, pmid = {41015376}, issn = {1532-2971}, mesh = {Animals ; Cats ; *Toxoplasmosis, Animal/metabolism/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Toxoplasma/physiology ; *Cat Diseases/parasitology/metabolism/microbiology ; Female ; Metabolomics ; Male ; Feces/microbiology ; Host-Parasite Interactions ; Multiomics ; }, abstract = {Toxoplasma gondii (T. gondii) is an obligate intracellular parasite with a complex life cycle that culminates in cats-its only definitive host. While its immunological impact is well studied, how T. gondii shapes the feline gut microbiota and systemic metabolism remains largely unexplored. To investigate host-parasite-microbiome interactions, we performed a multi-omics study combining metagenomic sequencing and untargeted serum metabolomics in cats before and after T. gondii infection. Fecal samples were used to construct a comprehensive microbial gene catalog and assess functional shifts, while serum samples were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) to capture systemic metabolic changes. Infection with T. gondii, particularly during its sexual replication phase, significantly disrupted gut microbial diversity, composition, and function. Functional annotation revealed downregulation of microbial genes involved in vitamin, cofactor, and energy metabolism, alongside upregulation of carbohydrate metabolism pathways. Concurrently, metabolomic profiling showed marked alterations in lipid profiles, amino acid pathways, and folate-mediated one-carbon metabolism. Integrated analysis uncovered strong correlations between specific microbial taxa-such as Bifidobacterium adolescentis and Ligilactobacillus animalis-and host metabolites, underscoring a tight link between microbial function and host metabolic responses to infection. To our knowledge, this is the first study to comprehensively map the microbiome and metabolic landscape of T. gondii infection in the feline host. Our findings reveal profound parasite-induced shifts in microbial function and systemic metabolism, offering new insights into the molecular interplay between host, parasite, and microbiota. These insights may inform future strategies for therapeutic modulation of host responses in toxoplasmosis.}, } @article {pmid41000006, year = {2026}, author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF}, title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.}, journal = {Plant, cell & environment}, volume = {49}, number = {1}, pages = {209-225}, doi = {10.1111/pce.70205}, pmid = {41000006}, issn = {1365-3040}, support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; }, mesh = {*Soil Microbiology ; *Poaceae/microbiology ; Rhizosphere ; *Microbiota ; Plant Roots/microbiology ; Metagenomics ; Biodiversity ; }, abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.}, } @article {pmid40974529, year = {2025}, author = {Tian, C and Tang, Z and Zhang, X and Yao, X and Li, Y and Zhuang, D and Luo, Y and Li, T and Bai, L and Zhao, F and Zhu, L and Shi, G and Jiang, P and Gong, Q and Zhou, H and Gao, H and Wu, Q and Sang, J and Liu, X and Li, X and Yu, L and Zhang, Z}, title = {Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.}, journal = {Science China. Life sciences}, volume = {68}, number = {12}, pages = {3646-3663}, pmid = {40974529}, issn = {1869-1889}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Tibet ; *Mammals/microbiology ; Humans ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/classification/drug effects ; }, abstract = {The mammalian species on the Tibetan Plateau are diverse and abundant, yet our understanding of their gut microbiome and antibiotic resistome remains limited. Here, we used metagenomics to analyse the gut microbiota of 2,561 mammals from the Tibetan Plateau, covering 14 species across six orders. Using de novo metagenome assembly, we reconstructed a total of 112,313 high- to medium-quality metagenomic assembly genomes (MAGs), representing 21,902 microbial species, 86% of which were unclassified. More than 8,000 nonredundant antibiotic resistance genes (ARGs) encompassing 28 types were identified in the gut microbiome of Tibetan Plateau mammals. We further conducted a risk assessment of these ARGs, identifying 334 nonredundant ARGs with high-risk characteristics related to human health. Importantly, seven cross-species horizontal gene transfer events involving high-risk ARGs were identified, three of which occurred between human and nonhuman mammalian gut microbiota. Additionally, we found that the abundance of ARGs in human gut microbiomes on the Tibetan Plateau was greater than that in those from eastern China, Europe, and the United States, whereas the abundance of ARGs in livestock gut microbiomes from the Tibetan Plateau was lower than that in livestock gut microbiomes from those regions. This study reveals that the gut microbiota of Tibetan Plateau mammals is a largely unexplored resource and a significant reservoir of ARGs, offering crucial insights into microbiome research and demonstrating potential public health implications.}, } @article {pmid40966389, year = {2025}, author = {Yan, Y and Zhou, X and Liu, L and Cai, Z and Penuelas, J and Huang, X}, title = {Soil Nutrient Enrichment Induces Trade-Offs in Bacterial Life-History Strategies Promoting Plant Productivity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {45}, pages = {e10066}, doi = {10.1002/advs.202510066}, pmid = {40966389}, issn = {2198-3844}, support = {U21A20226//National Natural Science Foundation of China/ ; 42430701//National Natural Science Foundation of China/ ; KYCX24_1825//Graduate Research and Innovation Projects of Jiangsu Province/ ; CX(23)1038//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; 2023YFD1902000//Key Technologies Research and Development Program/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; *Nutrients ; *Plant Development/physiology ; Microbiota ; }, abstract = {Despite the global prevalence of anthropogenic soil nutrient enrichment, its impacts on the trade-offs in microbial life-history strategies remain poorly understood, which is critical for agroecosystem productivity. Here, large-scale observational studies are integrated with controlled experiments to systematically evaluate how soil nutrient enrichment affects bacterial functional potential and growth-rate potential, ultimately determining microbial functions and plant productivity. These findings reveal stark contrasts between nutrient-poor open field (OF) and nutrient-rich greenhouse (GH) soils across multiple paired sites using 16S rRNA gene amplicon and metagenomic sequencing. OF microbial communities dominated by oligotrophs have higher taxonomic diversity, larger average genome sizes with abundant nutrient-cycling genes, but lower 16S ribosomal RNA gene operon copy numbers and predicted maximum growth rates. Conversely, GH communities dominated by copiotrophs have higher growth-rate potential, more plant-beneficial bacteria, and higher diversity of functional genes (e.g., biofilm formation, secondary metabolism, and bacterial chemotaxis), but lower bacterial functional potential. Controlled pot experiments demonstrate that GH-enriched microbial functions strongly promote plant growth, particularly under sufficient nutrients and abiotic stress. These findings reveal a nutrient-driven trade-off between bacterial functional potential and growth rate, with implications for optimizing nutrient management strategies in precision agriculture to enhance specific microbial functions and plant productivity.}, } @article {pmid40848091, year = {2025}, author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W}, title = {RNA-viromics unveils diverse RNA viral communities in Large-billed crows and Northern Ravens.}, journal = {Virus genes}, volume = {61}, number = {6}, pages = {657-667}, pmid = {40848091}, issn = {1572-994X}, support = {grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; grant No. 2022-HZ-812//program of science and technology international cooperation project of Qinghai province/ ; }, mesh = {Animals ; *Crows/virology ; *RNA Viruses/genetics/classification/isolation & purification ; *Virome/genetics ; Metagenomics ; Feces/virology ; RNA, Viral/genetics ; Phylogeny ; }, abstract = {Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.}, } @article {pmid40707808, year = {2025}, author = {Liu, Y and Shen, J and Zhang, X and Ping, F and Qyu, K and Shen, X}, title = {Xiaoyao Pill Regulates Gut Microbiota and Tryptophan Metabolism to Alleviate Depression Induced by Chronic Stress in Rats.}, journal = {Chinese journal of integrative medicine}, volume = {31}, number = {12}, pages = {1087-1096}, pmid = {40707808}, issn = {1993-0402}, mesh = {Animals ; *Tryptophan/metabolism ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Depression/drug therapy/microbiology/etiology/metabolism/blood ; Male ; *Stress, Psychological/complications/drug therapy ; Behavior, Animal/drug effects ; Rats ; Chronic Disease ; Hippocampus/pathology/drug effects ; }, abstract = {OBJECTIVE: To investigate the antidepressant effects of Xiaoyao Pill (XYP) by exploring its interactions with gut microbiota and tryptophan metabolism.

METHODS: Utilizing network pharmacology, the functional substance groups, key targets, and pathways of XYP in the treatment of depression were identified. The chronic unpredictable mild stress (CUMS) protocol was implemented in male Sprague-Dawley rats to establish depression model. Thirty rats were randomly divided into 3 groups according to their body weight (10 for each): control, CUMS and XYP groups (1.8 g/kg). After 28-day interventions, behavioral phenotyping including sucrose preference test (SPT) and open field test (OFT) were performed. Biochemical validation encompassed enzyme-linked immunosorbent assay for serum cortisol, hematoxylin-eosin histopathology, and immunohistochemistry. Liquid chromatography-mass spectrometry was utilized to profile serum metabolites, while fecal samples underwent metagenomic sequencing for gut microbiota characterization.

RESULTS: Network pharmacology studies predicted that key components can protect the nervous system by regulating inflammatory pathways through the blood-brain barrier. SPT and OFT showed that XYP treatment significantly ameliorated depressive-like behaviors (all P<0.05). XYP treatment also restored hippocampal neuronal density, increased serum neurotransmitter levels of neurotransmitters such as 5-hydroxytryptamine and vasoactive intestinal peptide, and while suppressing inflammatory markers such as tumor necrosis factor-alpha, interleukin-1 beta (IL-1 β), and IL-6 (all P<0.05). Metagenomics revealed significant restructuring of gut microbiota, notably the regulation of Parabacteroides distasonis (P<0.05). Non-targeted metabolomics analysis showed that the level of metabolites in the tryptophan and kynurenine pathway significantly changed (variable importance in the projection >1, P<0.05), and the change of metabolic flux was significantly correlated with behavioral improvement (P<0.05).

CONCLUSIONS: XYP exerts antidepressant effects by increasing neurotransmitter levels, reducing inflammatory makers and modulating Parabacteroides distasonis. Through further exploration of metabolomics, we found that XYP may play a protective role in depression by regulating tryptophan metabolism.}, } @article {pmid41339392, year = {2025}, author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R}, title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43082}, pmid = {41339392}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.}, } @article {pmid41339319, year = {2025}, author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , }, title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9904}, pmid = {41339319}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; }, abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age 7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.}, } @article {pmid41334589, year = {2025}, author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H}, title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593119}, doi = {10.1080/19490976.2025.2593119}, pmid = {41334589}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; }, abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.}, } @article {pmid41333806, year = {2025}, author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M}, title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1634631}, pmid = {41333806}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.

RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.

CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.}, } @article {pmid41332430, year = {2025}, author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML}, title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593076}, doi = {10.1080/19490976.2025.2593076}, pmid = {41332430}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; }, abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.}, } @article {pmid41328758, year = {2026}, author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA}, title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70086}, pmid = {41328758}, issn = {1755-0998}, support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; }, mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; }, abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.}, } @article {pmid41289310, year = {2025}, author = {Zhao, JX and Zheng, WB and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Yang, MT and Nan, FL and Jiang, J and Elsheikha, HM and Zhang, XX}, title = {Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {11}, pages = {e0013768}, doi = {10.1371/journal.pntd.0013768}, pmid = {41289310}, issn = {1935-2735}, mesh = {Animals ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; Rats ; *Toxoplasma/physiology ; Disease Models, Animal ; Male ; Metabolomics ; *Toxoplasmosis/metabolism/parasitology/microbiology ; *Toxoplasmosis, Animal/metabolism/microbiology/parasitology ; }, abstract = {Toxoplasma gondii infection disrupts the gut microbiota and host systemic metabolism, which plays a key role in the pathophysiology of toxoplasmosis. To investigate these interactions, we conducted metagenomic sequencing and untargeted serum metabolomics on 18 Sprague-Dawley rats across control, acute, and chronic stages of infection. De novo assembly of 148 Gb of high-quality reads produced a comprehensive non-redundant microbial gene catalog comprising over 5.7 million genes. Infection led to a marked reduction in microbial diversity and significant shifts in community structure. Chronic infection, in particular, was characterized by the enrichment of Lactobacillus johnsonii, Lactobacillus intestinalis, and Limosilactobacillus reuteri, alongside a marked depletion of Akkermansia muciniphila and Rothia nasimurium. These compositional changes coincided with reduced abundance of carbohydrate-active enzymes, suggesting impaired microbial metabolic capacity. Pathway analysis revealed distinct, stage- and gut-region-specific metabolic disruptions, including suppressed amino acid and energy metabolism, and enhanced glycan and carbohydrate pathways during chronic infection. Untargeted LC-MS/MS profiling uncovered 883 differentially abundant serum metabolites, enriched in pathways related to amino acid metabolism, bile acid transformation, and aromatic compound processing. Importantly, L. johnsonii and L. reuteri were positively correlated with metabolites implicated in immune modulation and oxidative stress response, whereas A. muciniphila showed negative associations. These findings demonstrate that T. gondii infection orchestrates a coordinated host-microbiota-metabolome network, advancing our understanding of disease mechanisms and pointing to novel microbial and metabolic targets for therapy.}, } @article {pmid41260114, year = {2025}, author = {Ahmad, W and Ray, R and Khan, AL}, title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.}, journal = {The Science of the total environment}, volume = {1007}, number = {}, pages = {180812}, doi = {10.1016/j.scitotenv.2025.180812}, pmid = {41260114}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Microbiota/drug effects ; *Silicates ; *Heat-Shock Response ; *Soil Microbiology ; *Glycine max/physiology/microbiology ; Hot Temperature ; }, abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.}, } @article {pmid41161274, year = {2025}, author = {Cai, X and Yuan, X and Singh, AK and Chen, C and Zhu, X and Liu, W}, title = {Tradeoffs between microbial life-history strategies drive soil carbon cycling during revegetation in karst ecosystems: A metagenomic perspective.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127802}, doi = {10.1016/j.jenvman.2025.127802}, pmid = {41161274}, issn = {1095-8630}, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Carbon Cycle ; Carbon ; Ecosystem ; Metagenomics ; Nitrogen ; Microbiota ; }, abstract = {Revegetation strongly influences the dynamics of soil organic carbon (SOC) and microbial communities. While microbial communities are known to drive carbon (C) cycling, the specific traits responsible for C stabilization and mineralization during the revegetation of degraded karst ecosystems are not well understood. This study used a combination of metagenomic and instrumental methods to investigate variations in soil physicochemical properties, organic C fractions, C-cycle microbial community traits (diversity, life strategies, and co-occurrence patterns), and C-cycling (fixation and degradation) genes across four karst ecosystems representing a revegetation chronosequence encompassing cropland, grassland, shrubland, and primary forest. Our findings demonstrated that revegetation increased total SOC and recalcitrant OC (ROC) contents, while it decreased dissolved inorganic nitrogen (DIN) and reduced the ratio of labile OC (LOC) to SOC. This indicates enhanced C pool stabilization and storage, alongside reduced soil nutrient availability. These shifts favored the development of C-cycle microbial communities with low diversity and high proportions of K-strategists, which efficiently utilize recalcitrant C under oligotrophic conditions. Consequently, the increased dominance of K-strategists redirected microbial resource acquisition, manifested in a 29 % decrease in C-fixation gene abundances (rTCA, WL, and DC/4-HB pathways) and a 27 % decrease in genes degrading labile C compounds (starch, hemicellulose, cellulose, and chitin). Conversely, genes involved in degrading recalcitrant C compounds (pectin and lignin) increased by 19 %. Furthermore, the elevated proportion of K-strategists enhanced the complexity and stability of microbial taxonomic and functional networks, potentially strengthening community resilience and nutrient cycling efficiency. These results reveal a causal link between shifts in the soil C pool and nutrient availability during revegetation and the subsequent reshaping of C-cycling microbial communities. Such restructured communities, in turn, drive the expression of genes associated with C stabilization and mineralization, thereby impacting the soil C pool. This study provides mechanistic insights into microbial-mediated biochemical processes governing soil C decomposition and stabilization in karst ecosystems, offering critical guidance for ecological restoration in these degraded and fragile regions.}, } @article {pmid41138387, year = {2025}, author = {Ochoa-Bernal, TG and Huber, DH and Espinosa-Solares, T}, title = {The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127698}, doi = {10.1016/j.jenvman.2025.127698}, pmid = {41138387}, issn = {1095-8630}, mesh = {*Methane/metabolism ; *Propionates/metabolism ; *Microbiota ; Animals ; Anaerobiosis ; Chickens ; Bacteria/metabolism ; }, abstract = {Propionate accumulation exerts a significant inhibitory effect on anaerobic digestion, which may result in the cessation of methane production. It has been reported that propionate can be degraded solely by a limited group of syntrophic propionate-oxidizing bacteria belonging to the following genera: Syntrophobacter, Smithella, and Pelotomaculum. Chicken litter is a substrate rich in protein and nitrogen, which makes it more susceptible by total ammonia nitrogen toxicity. This study aimed to elucidate the alterations and responses of microbial communities to extreme concentrations of propionate in co-digestion with chicken litter, thereby providing an extensive overview of community composition and functional potential through shotgun metagenomics sequencing. An enrichment process was conducted over 1220 days in co-digestion with chicken litter, utilizing a 10 L digester operating in semi-continuous mode and progressively increasing sodium propionate concentrations to create a selection pressure. The feed had 12 propionate concentration levels, varying from 0 to 24 g L[-1]; chicken litter was kept at 3 %. At the end of the enrichment process, it was surprisingly observed that the well known syntrophic bacteria were not present; instead, bacteria from the Proteiniphilum, Petrimonas, Vibrio, Corynebacterium, Coprobacter, Brachymacterium, Cloacimonas, and Treponema genera were found. Propionate degradation was mainly attributed to Corynebacterium stationis and Corynebacterium casei, through the ackA and pta enzymes. The putative lactate pathway was also detected by the pct enzyme. Methanogenic archaea increased relative abundance, particularly the genera Methanoculleus, Methanospirillum, Methanococcus, and Methanocella, synthesizing methane in several pathways, mainly hydrogenotrophic in the range from 0.189 to 0.320 mL CH4 kgvsadded[-1]. The enrichment using extreme propionate concentrations in co-digestion with chicken litter resulted in a microbial consortium that stabilized propionate degradation and methane production, which can be attributed to an adaptive functional redundancy.}, } @article {pmid41087617, year = {2025}, author = {Liu, M and Yang, L and Nan, D and Ma, L and Zhang, J and Liang, F and Yang, J and Liu, X}, title = {Hyperbaric oxygen treatment mitigates gut dysbiosis of mice with spinal cord injury.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {103}, number = {11-12}, pages = {1515-1532}, pmid = {41087617}, issn = {1432-1440}, support = {No. 82101964//National Natural Science Foundation of China/ ; No. 7202055//Natural Science Foundation of Beijing Municipality/ ; CYDXK 202208//Beijing Chao-Yang Hospital Multi-disciplinary Team Program/ ; }, mesh = {Animals ; *Spinal Cord Injuries/therapy/complications/metabolism/microbiology ; *Dysbiosis/therapy/etiology ; *Hyperbaric Oxygenation/methods ; *Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Cytokines/metabolism ; Feces/microbiology ; }, abstract = {Gut dysbiosis impacts the recovery of neurological function after spinal cord injury (SCI). Hyperbaric oxygen (HBO) can alleviate SCI, but its effects on the gut microbiota post-SCI remain unclear. This study aimed to clarify the impact of HBO on SCI-induced gut dysbiosis and to explore the mechanisms of locomotor recovery in HBO-treated SCI mice. After establishing different groups of mouse models, bacterial cultures and Basso Mouse Scale (BMS) scores were performed at various time points post-SCI. Intestinal tissues were collected for intestinal permeability assay, histological analysis, immunofluorescence, and qPCR analysis. Flow cytometry and ELISA were used to detect immune-inflammatory cells and cytokines in intestinal tissue. The composition of gut microbiota in fecal samples from each group was also analyzed. Spinal cord tissues were collected for immunofluorescence and untargeted metabolomics analysis. Spearman correlation analysis was used to correlate differential microbiota with differential metabolites. Our results showed that the expression of tight junction proteins was increased after HBO treatment in SCI mice. Metagenomic analysis of the fecal DNA revealed that HBO altered intestinal bacterial composition. Differential metabolites were mainly enriched in pathways, such as glycerophospholipid metabolism, steroid biosynthesis, and glycolysis/gluconeogenesis. Moreover, differential microbiota showed a strong correlation with differential metabolites related to glycerophospholipids. HBO treatment significantly inhibited immune cells and inflammatory cytokines in the gut after SCI. In addition, HBO treatment significantly increased BMS scores and body weight, and repaired damaged cholinergic neurons. Antibiotic-induced gut dysbiosis impaired the recovery of locomotor function and exacerbated intraspinal pathology. However, these effects could be mitigated by HBO treatment. Overall, HBO treatment may improve neurological recovery through multiple regulatory mechanisms including alleviating gut dysbiosis, reducing intestinal inflammation, and rectifying glycerophospholipid metabolic disorders after SCI. These findings highlight HBO as a promising therapeutic strategy for SCI treatment and support its clinical application. KEY MESSAGES: The intestinal microbiota composition of mice changed after SCI. HBO treatment could preserve intestinal barrier integrity, modulate the composition of intestinal microbiota, rectify glycerophospholipid metabolic disorders, and reduce intestinal immune inflammatory responses. Intestinal microbiota identified as the target for HBO therapeutic in SCI recovery. Alleviating SCI-induced gut dysbiosis may be one of the mechanisms underlying the beneficial effect of HBO on neurological functions.}, } @article {pmid41058431, year = {2025}, author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV}, title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.}, journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)}, volume = {43}, number = {10}, pages = {698-708}, doi = {10.1016/j.eimce.2025.09.011}, pmid = {41058431}, issn = {2529-993X}, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Artificial Intelligence ; }, abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.}, } @article {pmid41016664, year = {2025}, author = {Dong, Y and Zheng, JS and Yang, Y and Wang, T and Li, F and Wu, P and Lai, Y and Wang, Y and He, X and Zhang, P and Zhang, S and Wu, N and Li, S and Yuan, J and Shan, D and Liu, X and Liu, G and Hu, Y and Pan, A and Pan, XF}, title = {Associations between combined healthy lifestyle and adverse birth outcomes in 2 prospective cohorts: roles of gut microbiota and serum metabolites.}, journal = {The American journal of clinical nutrition}, volume = {122}, number = {6}, pages = {1735-1747}, doi = {10.1016/j.ajcnut.2025.09.036}, pmid = {41016664}, issn = {1938-3207}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Adult ; Prospective Studies ; Pregnancy ; Male ; *Healthy Lifestyle ; Infant, Newborn ; *Pregnancy Outcome ; Metabolome ; Cohort Studies ; Birth Cohort ; }, abstract = {BACKGROUND: Maternal lifestyle factors are reported to be associated with adverse birth outcomes (ABOs). These factors may also influence gut microbiota composition and serum metabolic profiles.

OBJECTIVES: The aim of this study was to investigate the associations between combined healthy lifestyle and ABOs, and the mediating roles of gut microbiota and serum metabolites.

METHODS: This study was conducted based on the Tongji-Huaxi-Shuangliu Birth Cohort (THSBC), comprising 1086 participants with repeated multiomics data collected at 3 time points. An independent validation was performed using 161 participants from the Huaxi Birth Cohort, with available multiomics data at 5 time points. Participants were classified into 3 lifestyle categories (unhealthy, low healthy, and highly healthy) according to diet, physical activity, smoking, drinking, sleep, and body mass index. Gut microbiota were characterized using 16S rRNA gene sequencing in the THSBC and metagenomics in the Huaxi Birth Cohort, whereas serum metabolites were profiled using untargeted liquid chromatography-mass spectrometry. Clinical data on birth outcomes, such as gestational age, birth weight, and sex, were collected in the THSBC.

RESULTS: A highly healthy lifestyle was associated with lower risks of macrosomia (MAC) [odds ratio (OR): 0.43; 95% confidence interval (CI): 0.33, 0.57], preterm birth (PTB) (OR: 0.60; 95% CI: 0.46, 0.79), and large for gestational age (LGA) (OR: 0.44; 95% CI: 0.35, 0.56). Among the identified mediators, gut microbiota and serum metabolites, including Eisenbergiella, Tyzzerella, Megamonas, pro-Ile, and 1-amino-1-cyclobutane-carboxylic acid, were negatively associated with a healthy lifestyle, whereas Lachnospiraceae NK4A136 group, 4-methoxyestrone, and lysophosphatidylcholine [LPC(0:0/18:3)] were positively associated. Mediation analyses showed that Eisenbergiella and 4-methoxyestrone explained 11.4% and 13.0% of the inverse association between a highly healthy lifestyle and PTB, respectively, whereas the other microbiota and metabolites mediated 5%-7% of the associations with MAC and LGA.

CONCLUSIONS: Maternal healthy lifestyle is associated with lower risk of ABOs, with gut microbiota and serum metabolites serving as important mediators in these relationships.}, } @article {pmid40961238, year = {2025}, author = {Shalash, A and Ezzeldin, S and Hashish, S and Salah, Y and Dawood, NL and Moustafa, A and Salama, M}, title = {Gut microbial shifts toward inflammation in Parkinson's disease: Insights from pilot shotgun metagenomics Egyptian cohort.}, journal = {Journal of Parkinson's disease}, volume = {15}, number = {8}, pages = {1540-1543}, doi = {10.1177/1877718X251370156}, pmid = {40961238}, issn = {1877-718X}, mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Pilot Projects ; Metagenomics ; Male ; Middle Aged ; Female ; Egypt ; Aged ; *Inflammation/microbiology ; Feces/microbiology ; Cohort Studies ; *Dysbiosis/microbiology ; }, abstract = {Gut microbiome alterations are increasingly linked to Parkinson's disease (PD), yet regional signatures remain underexplored. We performed shotgun metagenomic sequencing of stool samples from Egyptian PD patients and healthy controls. PD patients exhibited depletion of short-chain fatty acid-producing taxa, and enrichment of pathobionts. Our findings suggested a pro-inflammatory gut shift in PD and emphasized the need for geographically diverse microbiome studies. While limited in sample size (n = 7 PD patients and n = 6 controls), this pilot addressed a critical gap in African PD microbiome research.}, } @article {pmid40389632, year = {2025}, author = {Doyle, B and Reynolds, GZM and Dvorak, M and Maghini, DG and Natarajan, A and Bhatt, AS}, title = {Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR.}, journal = {Nature protocols}, volume = {20}, number = {12}, pages = {3441-3476}, pmid = {40389632}, issn = {1750-2799}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32GM007276//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; D43TW010540//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Polymerase Chain Reaction/methods ; *Real-Time Polymerase Chain Reaction/methods ; *Microbiota/genetics ; *Bacteria/genetics ; *Prokaryotic Cells ; }, abstract = {Measurements of prokaryotic absolute abundance can provide important insights into human gut microbiome biology and correct misinterpretations of relative abundance data. Despite the existence of several relatively well-established methods for making these measurements, most microbiome studies do not report absolute abundance. To enable researchers equipped with standard molecular biology capabilities to incorporate absolute quantification into their microbiome studies, we present a detailed, step-by-step protocol for rigorous and reproducible quantification of prokaryotic concentration in stool samples. We include methods for measuring stool sample moisture content, quantifying the concentration of the 16S rRNA prokaryotic marker gene by qPCR or digital droplet PCR (ddPCR) and analyzing the resulting data. We also highlight and provide strategies to overcome common pitfalls of the quantification method, such as 16S rRNA gene contamination. The final output of this approach is 16S rRNA copies per wet or dry gram of stool. In cases where samples have matched metagenomic sequencing information, data can be converted into absolute concentration of prokaryotes and taxon-specific absolute concentrations. To enable researchers to choose the appropriate method for their specific applications, we also compare and contrast our qPCR and ddPCR methods. In 4 days, ~80 samples can be taken from frozen stool to absolute concentration by using qPCR or ddPCR without the need for resequencing. Overall, this protocol provides a sensitive and straightforward way to measure the absolute concentration of prokaryotes in human gut microbiome samples stored with or without preservative.}, } @article {pmid41328492, year = {2025}, author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C}, title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2592423}, doi = {10.1080/19490976.2025.2592423}, pmid = {41328492}, issn = {1949-0984}, mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation & purification/genetics/growth & development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; }, abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.

METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at < 33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.

RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).

CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.}, } @article {pmid41328416, year = {2025}, author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR}, title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72546}, pmid = {41328416}, issn = {2045-7758}, abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.}, } @article {pmid41328248, year = {2025}, author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN}, title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.}, journal = {Journal of advanced veterinary and animal research}, volume = {12}, number = {3}, pages = {717-727}, pmid = {41328248}, issn = {2311-7710}, abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.

MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.

RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.

CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.}, } @article {pmid41328030, year = {2025}, author = {Hickman, B and Korpela, K}, title = {Impact of data compositionality on the detection of microbiota responses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2590841}, doi = {10.1080/19490976.2025.2590841}, pmid = {41328030}, issn = {1949-0984}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; }, abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.}, } @article {pmid41328016, year = {2025}, author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O}, title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2587968}, doi = {10.1080/19490976.2025.2587968}, pmid = {41328016}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; }, abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).}, } @article {pmid41326129, year = {2026}, author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S}, title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.}, journal = {Pesticide biochemistry and physiology}, volume = {216}, number = {Pt 1}, pages = {106807}, doi = {10.1016/j.pestbp.2025.106807}, pmid = {41326129}, issn = {1095-9939}, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; }, abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.}, } @article {pmid41205292, year = {2026}, author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA}, title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118904}, doi = {10.1016/j.marpolbul.2025.118904}, pmid = {41205292}, issn = {1879-3363}, mesh = {*Petroleum Pollution ; *Geologic Sediments/microbiology/chemistry ; *Bacteria ; Biodegradation, Environmental ; *Water Pollutants, Chemical/analysis ; *Ecosystem ; Petroleum ; Environmental Monitoring ; Hydrocarbons/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; *Microbiota ; }, abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.}, } @article {pmid41193635, year = {2025}, author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R}, title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.}, journal = {Nature microbiology}, volume = {10}, number = {12}, pages = {3245-3257}, pmid = {41193635}, issn = {2058-5276}, support = {991222//Simons Foundation/ ; }, mesh = {*Seawater/virology ; *Genome, Viral ; *Genomics/methods ; Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Microbiota/genetics ; Metagenome ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.}, } @article {pmid41092847, year = {2025}, author = {Zhang, Y and Su, K and Munir, F and Wang, W and Liang, X and Wang, J and Hua, J and Ma, W}, title = {Gut microbiome metagenomics in diarrheic and healthy Simmental cattle from Ningxia Province, China.}, journal = {Research in veterinary science}, volume = {197}, number = {}, pages = {105922}, doi = {10.1016/j.rvsc.2025.105922}, pmid = {41092847}, issn = {1532-2661}, mesh = {Animals ; Cattle ; China ; *Cattle Diseases/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Diarrhea/veterinary/microbiology ; Feces/microbiology ; Bacteria/genetics/classification ; }, abstract = {INTRODUCTION: The gut microbiome plays a crucial role in health and disease. This study aims to investigate the composition, characteristics, and functional diversity of the intestinal microbiome by performing metagenomic sequencing on fecal samples from diarrheic and healthy Simmental cattle.

RESULTS: This study compared the gut microbiome differences between two groups of Simmental cattle (5 diarrheic and 20 healthy) in Ningxia province, China. Metagenomic analysis revealed higher microbial heterogeneity in the diarrheic group, likely reflecting pathogen-driven ecological disruption, whereas the healthy group was dominated by butyrate-producing and fiber-degrading bacteria, maintaining intestinal homeostasis. Antibiotic resistance gene analysis detected glycopeptide resistance genes in both groups, but the healthy group also carried aminoglycoside/tetracycline resistance genes and poxtA. KEGG pathway analysis showed that the diarrheic group was enriched in purine synthesis-related pathways, while the healthy group exhibited dominant metabolic pathways such as glutamine synthase. Virulence factor analysis indicated that the diarrheic group had higher abundances of capsular polysaccharides and type IV secretion systems, potentially promoting bacterial colonization and immune evasion. In summary, diarrheic cattle harbored a gut microbiome dominated by opportunistic pathogens, accompanied by metabolic dysregulation and antimicrobial resistance risks, whereas healthy cattle maintained a microbial community rich in short-chain fatty acid producers. This study provides a theoretical foundation for gut microbiome modulation and antimicrobial resistance control in ruminants.

CONCLUSION: This study revealed distinct gut microbiome composition and function between diarrheic and healthy cattle through sequencing analysis. The findings offer insights for ruminant diarrhea management and provide a basis for developing more scientific antibiotic management strategies in animal husbandry.}, } @article {pmid40990171, year = {2025}, author = {Sehgal, N and Pajuelo, MJ and Gilman, RH and Pickering, AJ and Earl, AM and Worby, CJ and Nadimpalli, ML}, title = {Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {80}, number = {12}, pages = {3248-3256}, doi = {10.1093/jac/dkaf358}, pmid = {40990171}, issn = {1460-2091}, support = {R01AI108695-01A/GF/NIH HHS/United States ; KL2TR002545/GF/NIH HHS/United States ; U19AI110818/GF/NIH HHS/United States ; 5T32ES012870/GF/NIH HHS/United States ; //Emory University/ ; //MP3 Initiative/ ; }, mesh = {Humans ; Peru ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Infant ; Prospective Studies ; Feces/microbiology ; Male ; Female ; *Bacteria/drug effects/genetics/classification ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; }, abstract = {BACKGROUND: The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where antibiotic consumption is exceptionally common.

OBJECTIVES: We characterized the effects of antibiotics commonly used by Peruvian children (i.e. amoxicillin, azithromycin, cefalexin, trimethoprim/sulfamethoxazole) on the α-diversity, β-diversity and abundance of gut genera and antibiotic resistance genes (ARGs) from 3 to 16 months.

METHODS: This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-19. Stools collected at 3, 6, 7, 9, 12 and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40 662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, we examined associations of recent antibiotic use with richness, diversity and abundance of gut genera and ARGs over time.

RESULTS: Each additional recent antibiotic course decreased Bifidobacterium and Dialister abundance and increased Veillonella abundance, although gut richness and diversity were not affected. Recent use of amoxicillin, azithromycin, cefalexin or trimethoprim/sulfamethoxazole, specifically, did not impact gut microbiome measures. Amoxicillin, azithromycin and trimethoprim/sulfamethoxazole significantly enriched multiple ARGs and amoxicillin use significantly increased total ARGs.

CONCLUSIONS: Common antibiotics like amoxicillin and azithromycin appear to be key drivers of the paediatric gut resistome. Resistome perturbations appeared to be stronger, or persist for longer, than gut microbiome effects in this middle-income country setting.}, } @article {pmid40764207, year = {2026}, author = {Jiang, H and Zhang, J and Li, S and Kwok, T and Ng, SC and Lee, ATC and Xu, Z}, title = {Dietary index for gut microbiota (DI-GM) and cognitive function: NHANES findings and validation in a Hong Kong cohort with metagenomic data.}, journal = {The journal of prevention of Alzheimer's disease}, volume = {13}, number = {1}, pages = {100319}, doi = {10.1016/j.tjpad.2025.100319}, pmid = {40764207}, issn = {2426-0266}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Hong Kong ; Male ; Female ; *Cognition/physiology ; Aged ; *Diet ; Nutrition Surveys ; Cohort Studies ; Metagenomics ; Middle Aged ; *Cognitive Dysfunction ; Neuropsychological Tests ; }, abstract = {BACKGROUND: The diet-gut-microbiota-brain axis is critical for maintaining brain health. The Dietary Index for Gut Microbiota (DI-GM), comprising beneficial and unfavorable components, may serve as a proxy for this connection, yet its association with cognition remains underexplored.

METHODS: This study examined the relationship between DI-GM, its components, and cognitive function in older adults using data from the National Health and Nutrition Examination Survey (NHANES). Findings were validated in an independent Hong Kong osteoporosis cohort (OS cohort) with gut metagenomic data to assess of microbiota's mediating role in diet-cognition relationship. Cognitive assessment in NHANES utilized the Consortium to Establish a Registry for Alzheimer's Disease (CERAD), Animal Fluency Test (AFT), and Digit Symbol Substitution Test (DSST), while the OS cohort employed the Hong Kong version of the Montreal Cognitive Assessment (HK-MoCA). DI-GM was calculated from 24-hour dietary recalls. The diet-cognition associations were assessed by weighted multivariate regressions, supplemented by restricted cubic spline (RCS), subgroup, correlation network, and mediation analyses.

RESULTS: Higher DI-GM was significantly associated with better performance on DSST (OR=0.90; 95 % CI: 0.82, 0.99; p = 0.033). The beneficial-to-gut-microbiota score (BGMS) associated with lower psychometric mild cognitive impairment (p-MCI) risk (OR=0.88; 95 % CI: 0.80, 0.98; p = 0.022) and better CERAD immediate and delayed recall and DSST (all p < 0.05). The beneficial-to-gut-microbiota components like dietary fiber demonstrated protective effects across cognitive domains, while refined grains was associated with poorer cognition. In the OS cohort, higher dietary fiber intake correlated with higher HK-MoCA score (p < 0.05) and increased abundance of fermenting bacteria. Among these species, Eubacterium ventriosum mediated the beneficial effect of dietary fiber intake on dementia risk reduction, with an indirect effect of -0.014 (95 % CrI: -0.040, -0.001), accounting for approximately 12.7 % of the total effect.

CONCLUSION: Higher adherence to beneficial-to-gut-microbiota dietary patterns, as reflected by DI-GM, was associated with better cognitive function in older adults. These findings highlight the importance of a gut-microbiota-targeted diet in maintaining cognitive health.}, } @article {pmid41322254, year = {2025}, author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q}, title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.}, journal = {Marine life science & technology}, volume = {7}, number = {4}, pages = {670-681}, pmid = {41322254}, issn = {2662-1746}, abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.}, } @article {pmid41321415, year = {2025}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D}, title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf199}, pmid = {41321415}, issn = {2730-6151}, abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.}, } @article {pmid41315430, year = {2025}, author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D}, title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42704}, pmid = {41315430}, issn = {2045-2322}, support = {R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; }, mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; }, abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).}, } @article {pmid41270667, year = {2025}, author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T}, title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.}, journal = {Chemosphere}, volume = {393}, number = {}, pages = {144767}, doi = {10.1016/j.chemosphere.2025.144767}, pmid = {41270667}, issn = {1879-1298}, mesh = {*Methylmercury Compounds/analysis ; *Oryza/chemistry ; *Mercury/analysis ; *Soil Pollutants/analysis ; *Soil Microbiology ; Soil/chemistry ; Microbiota ; Environmental Monitoring ; }, abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.}, } @article {pmid41206461, year = {2025}, author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H}, title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {32}, number = {6}, pages = {}, doi = {10.1093/dnares/dsaf032}, pmid = {41206461}, issn = {1756-1663}, support = {//Government of/ ; JPJ009237//Japan/ ; //Bio-oriented Technology Research Advancement Institution/ ; }, mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Microbiota ; Plant Roots/microbiology ; *Bacteria/genetics/classification ; Metagenome ; *Genomics/methods ; Single-Cell Analysis/methods ; Genome, Bacterial ; }, abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogues in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.}, } @article {pmid41138814, year = {2025}, author = {Matsumoto, A and Yoshimura, Y and Wakabayashi, H and Nagano, F and Shimazu, S and Kido, Y and Shiraishi, A and Hamada, T and Yoneda, K and Maeda, K}, title = {Polypharmacy is associated with altered gut microbiota diversity in older post-stroke inpatients.}, journal = {Clinical nutrition ESPEN}, volume = {70}, number = {}, pages = {427-433}, doi = {10.1016/j.clnesp.2025.10.015}, pmid = {41138814}, issn = {2405-4577}, mesh = {Humans ; *Polypharmacy ; Male ; Aged ; *Gastrointestinal Microbiome/drug effects ; Female ; Cross-Sectional Studies ; *Stroke/microbiology/drug therapy ; Aged, 80 and over ; Inpatients ; Feces/microbiology ; Phylogeny ; Stroke Rehabilitation ; }, abstract = {RATIONALE: Gut microbiota diversity plays a crucial role in various health outcomes, including metabolic regulation and nutritional status. Polypharmacy, common among older adults, has been linked to adverse clinical outcomes, yet its impact on gut microbiota diversity remains poorly understood. This study aimed to investigate the association between polypharmacy and gut microbiota diversity in older post-stroke patients.

METHODS: This cross-sectional study included post-stroke inpatients aged 65 years or older undergoing rehabilitation. Polypharmacy was defined as the prescription of five or more drugs. Metagenomic analysis of DNA from patient fecal samples was conducted, calculating three alpha diversity indices: the Shannon Diversity Index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analysis was used to determine whether polypharmacy was independently associated with the gut microbiota diversity upon admission, adjusting for potential confounders.

RESULTS: A total of 156 patients (mean age 78.4 years; 55.8 % male) were analyzed. The median number of medications taken on admission was 6 (4-8), and 69.9 % of patients had polypharmacy. Polypharmacy was independently associated with decreased Shannon Diversity Index (β = -0.202, p = 0.019). No statistically significant association was found with Observed OTUs (β = -0.159, p = 0.067) and Faith's PD (β = -0.38, p = 0.111).

CONCLUSIONS: Polypharmacy is associated with qualitative alterations in the gut microbiota of older post-stroke patients, with a potential negative trend in quantitative alterations and phylogenetic classification. The findings underscore the need to consider the impact of polypharmacy on the gut microbiome in stroke management.}, } @article {pmid41125958, year = {2025}, author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, TJ and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G}, title = {Long-read metagenomics for strain tracking after faecal microbiota transplant.}, journal = {Nature microbiology}, volume = {10}, number = {12}, pages = {3258-3271}, pmid = {41125958}, issn = {2058-5276}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; R35 GM139655/GM/NIGMS NIH HHS/United States ; }, mesh = {*Fecal Microbiota Transplantation ; *Metagenomics/methods ; Humans ; Clostridium Infections/therapy/microbiology ; Feces/microbiology ; Clostridioides difficile/genetics/classification/isolation & purification ; Inflammatory Bowel Diseases/therapy/microbiology ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; }, abstract = {Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrent Clostridioides difficile infection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations.}, } @article {pmid40847462, year = {2025}, author = {Ma, H and Wang, M and Feng, Y and Zhang, W and Wang, W and Xie, Y and Kong, G and Feng, J and Wang, P and Wang, Q and Huang, X}, title = {Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.}, journal = {FEBS open bio}, volume = {15}, number = {12}, pages = {2001-2020}, doi = {10.1002/2211-5463.70105}, pmid = {40847462}, issn = {2211-5463}, support = {GSWSKY2020-50//Gansu Provincial Health Commission, Provincial Health Industry Research Project/ ; 20240050058//Lanzhou University Student Innovation and Entrepreneurship Action Plan Project/ ; CY2023-QN-B17//Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University in 2023/ ; }, mesh = {Humans ; *Appendicitis/microbiology ; Male ; Female ; *Appendix/microbiology ; Adult ; Metagenomics/methods ; Middle Aged ; Bacteria/genetics/classification/isolation & purification ; Gastrointestinal Microbiome/genetics ; }, abstract = {Relatively little is known about the microbial variations within the human appendix niche. To overcome this knowledge gap, we employed endoscopic retrograde appendicitis treatment (ERAT) technology to collect microbial samples from the appendix lumen, followed by shotgun metagenomic sequencing on participants with acute appendicitis without antibiotic treatment. Compared to the cecum and terminal ileum, the appendix had a higher abundance at the genus level of Sphingobium, Leptotrichia and Oribacterium, as well as a significant increase in species-level abundance of oral bacteria, including Streptococcus sanguinis, Streptococcus australis, Streptococcus sp. A12, Leptotrichia sp. oral taxon 215, Veillonella dispar, Veillonella infantium and Oribacterium sinus. Pearson correlation analysis showed that bacterial species abundant in the appendix, such as Acinetobacter johnsonii, Sphingobium yanoikuyae and Agrobacterium tumefaciens, had negative correlations with the top five most abundant Gene Ontology (GO) categories (molecular function, biological process and cellular component). Conversely, species underrepresented in the appendix, including Mogibacterium diversum, Streptococcus sanguinis, Megasphaera micronuciformis and Actinomyces graevenitzii, had significant positive correlations with these GO categories. Our results show that ERAT technology can be used to improve sampling and microbiome profiling in the appendix. Furthermore, this in-depth microbial characterization could inform clinicians during antibiotic prescription. However, further large sample size studies are required to validate these results.}, } @article {pmid40525692, year = {2025}, author = {Jarrett, ZS and Xia, H and O'Neil, ER and Lonergan, TP and Gonzales, M and Sobieszczyk, M and Gibbons, TF and Marcus, JE}, title = {Characterizing Microbiome Changes in Veno-Venous Extracorporeal Membrane Oxygenation: A Case Report of Multidrug-Resistant Bacteremia.}, journal = {ASAIO journal (American Society for Artificial Internal Organs : 1992)}, volume = {71}, number = {12}, pages = {e252-e255}, doi = {10.1097/MAT.0000000000002479}, pmid = {40525692}, issn = {1538-943X}, support = {//Clinical Investigations & Research Support (CIRS)/ ; }, mesh = {Humans ; *Extracorporeal Membrane Oxygenation/adverse effects ; Male ; *Bacteremia/microbiology/drug therapy/etiology ; Middle Aged ; *Drug Resistance, Multiple, Bacterial ; *Microbiota ; Pseudomonas aeruginosa/drug effects/isolation & purification ; Fatal Outcome ; Anti-Bacterial Agents/therapeutic use ; Enterobacter cloacae/isolation & purification ; Pseudomonas Infections/microbiology ; }, abstract = {Microbiome analysis using metagenomics next-generation sequencing (mNGS) is rarely performed in patients receiving extracorporeal membrane oxygenation (ECMO). Patient body sites were swabbed within 72 hours of ECMO cannulation and weekly during ECMO course. Specimens underwent 16S sequencing to identify the microbiome along with mNGS to determine antimicrobial resistance genes. Fifty-two year old male who suffered polytraumatic injuries and developed acute respiratory syndrome was placed on veno-venous (VV) ECMO to treat severe respiratory failure. On ECMO day 1, the patient was undergoing treatment for urinary tract infection due to susceptible Pseudomonas aeruginosa (PsA). On ECMO day 22, the patient developed fulminant septic shock and tracheal aspirate and blood cultures both grew MDR PsA and Enterobacter cloacae complex (ECC) and ultimately died on day 23. There were significant microbiome and antimicrobial resistance changes that preceded sepsis on day 22, as evidenced by the increase in oral PsA colonization and expansion of resistance genes, such as KPC and OXA-50 , which suggest several possible reservoirs for infection outside of the circuit. Further application of these methods is needed to understand microbiome changes in ECMO and ultimately guide infection prevention efforts.}, } @article {pmid41315331, year = {2025}, author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S}, title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {223}, pmid = {41315331}, issn = {2055-5008}, support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; }, mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; }, abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.}, } @article {pmid41242205, year = {2026}, author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D}, title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128397}, doi = {10.1016/j.micres.2025.128397}, pmid = {41242205}, issn = {1618-0623}, mesh = {*Rhizosphere ; Soil Microbiology ; *Salt-Tolerant Plants/microbiology/genetics ; Bacteria/genetics/classification/isolation & purification/metabolism ; *Salt Stress/genetics ; *Microbiota/genetics ; Soil/chemistry ; Salt Tolerance/genetics ; Metagenomics ; Fungi/genetics/classification/isolation & purification ; Plant Roots/microbiology ; Salinity ; Poaceae/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.}, } @article {pmid41192043, year = {2026}, author = {Kumar, A and Xu, C and Dakal, TC}, title = {Microbiome based precision medicine through integrated multiomics and machine learning.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128384}, doi = {10.1016/j.micres.2025.128384}, pmid = {41192043}, issn = {1618-0623}, mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Metabolomics/methods ; Proteomics/methods ; Dysbiosis/microbiology ; Inflammatory Bowel Diseases/microbiology ; Multiomics ; }, abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.}, } @article {pmid41175696, year = {2026}, author = {Li, N and Zhang, Y and Qu, Z and Xu, J and Ming, A and Sun, H and Huang, L}, title = {Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128381}, doi = {10.1016/j.micres.2025.128381}, pmid = {41175696}, issn = {1618-0623}, mesh = {*Eucalyptus/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Biodiversity ; Soil/chemistry ; Phosphorus/metabolism ; Metabolomics ; Microbiota ; Metagenomics ; Nitrogen/metabolism ; Nitrogen Fixation ; }, abstract = {The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)-which plays a key role in soil phosphorus cycle-was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (rbcL and ppc) and phosphorus cycle (phoP and ppk2). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.}, } @article {pmid41258495, year = {2025}, author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A}, title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {136}, pmid = {41258495}, issn = {1432-184X}, support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; }, mesh = {Animals ; *Microbiota ; *Symbiosis ; *Gastropoda/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Bacteriophages/isolation & purification/genetics/classification ; Phylogeny ; }, abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.}, } @article {pmid41252249, year = {2025}, author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS}, title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116573}, doi = {10.1016/j.celrep.2025.116573}, pmid = {41252249}, issn = {2211-1247}, mesh = {Humans ; Indonesia ; *Rural Population ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; *Urban Population ; Metagenome ; *Microbiota ; Male ; Female ; }, abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.}, } @article {pmid41241073, year = {2026}, author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W}, title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.}, journal = {Journal of affective disorders}, volume = {394}, number = {Pt B}, pages = {120709}, doi = {10.1016/j.jad.2025.120709}, pmid = {41241073}, issn = {1573-2517}, mesh = {Humans ; Male ; *Depressive Disorder, Major/drug therapy/microbiology ; *Gastrointestinal Microbiome/genetics/drug effects ; Female ; Adult ; Prospective Studies ; Middle Aged ; *Selective Serotonin Reuptake Inhibitors/therapeutic use ; Metagenomics ; *Antidepressive Agents/therapeutic use ; Feces/microbiology ; *Serotonin and Noradrenaline Reuptake Inhibitors/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.

METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12 ± 15.79 years, 8 males), while 14 were non-responders (40.14 ± 17.28 years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).

RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.

CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.}, } @article {pmid41232906, year = {2026}, author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M}, title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.}, journal = {Environmental research}, volume = {288}, number = {Pt 2}, pages = {123287}, doi = {10.1016/j.envres.2025.123287}, pmid = {41232906}, issn = {1096-0953}, mesh = {*Wastewater/microbiology ; India ; Metagenomics ; *Microbiota ; *Drug Resistance, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13 % of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49 %), macrolide-lincosamide-streptogramin (15.84 %), beta-lactam (7.95 %), and tetracycline (6.52 %). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.}, } @article {pmid41166306, year = {2025}, author = {Zhang, ZF and Huang, JE and Phurbu, D and Qu, ZS and Liu, F and Cai, L}, title = {A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116483}, doi = {10.1016/j.celrep.2025.116483}, pmid = {41166306}, issn = {2211-1247}, mesh = {*Lakes/microbiology ; *Salinity ; *Metagenomics/methods ; *Adaptation, Physiological/genetics ; *Metagenome/genetics ; Salt Tolerance/genetics ; China ; Biodiversity ; Geologic Sediments/microbiology ; Bacteria/genetics/classification ; }, abstract = {The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.}, } @article {pmid41138185, year = {2025}, author = {Waschina, S and Pagel, J and Seeger, K and Pasderski, E and Rühlemann, M and Froitzheim, S and Künzel, S and Sommer, F and Franzenburg, S and Fortmann, I and Sugihara, F and Faust, K and Marissen, J and Demmert, M and Baines, JF and Göpel, W and Herting, E and Kaleta, C and Rupp, J and Härtel, C}, title = {Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116431}, doi = {10.1016/j.celrep.2025.116431}, pmid = {41138185}, issn = {2211-1247}, mesh = {Humans ; *Probiotics/therapeutic use ; *Sepsis/microbiology/prevention & control ; Infant, Newborn ; Female ; Male ; Gastrointestinal Microbiome ; Infant, Very Low Birth Weight ; Infant ; Metabolome ; Risk Factors ; *Bacteria/metabolism ; }, abstract = {The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed intestinal metagenome and metabolome data in VLBWIs during the period of highest vulnerability of LOS. Using a unit's policy change to routinely administer B. longum subspecies infantis plus Lactobacillus acidophilus as natural experiment, we compared 97 infants (including 38 LOS cases) after change with 78 infants (including 32 LOS cases) before. Probiotic supplementation was associated with more beneficial bacteria and reduced abundance of nosocomial pathobionts, such as Klebsiella spp. Infants in the probiotic group had significantly lower concentrations of B. longum fermentation products prior to sepsis diagnosis than matched non-LOS cases (acetate: padj = 0.0049; lactate: padj = 0.048). Modulation of the gut metabolic milieu is an interesting target for LOS prevention.}, } @article {pmid41138182, year = {2025}, author = {Gao, SM and Lan, LY and Yang, L and Chen, T and Fan, PF}, title = {Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116477}, doi = {10.1016/j.celrep.2025.116477}, pmid = {41138182}, issn = {2211-1247}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; *Primates/microbiology ; Feces/microbiology ; *Microbial Interactions ; Metagenome ; Bacteria/genetics/metabolism/classification ; }, abstract = {Gut microbiota often undergo metabolic cross-feeding and resource competition. However, our understanding of global variations in these interactions and their implications for host health remain elusive. By analyzing a microbial genome catalog from 841 fecal metagenomes across 53 primate species worldwide, we identified key microbiota assigned to two taxa, i.e., Bacillota_A and Pseudomonadota, which well predicted the trade-off of community-level interaction types between metabolic competition and cooperation. Specifically, Bacillota_A species were inherently competitive and amino acid auxotrophic and typically found in anaerobic habitats. In contrast, members of Pseudomonadota were inherently cooperative, siderophore producers, and more abundant in aerobic conditions. Random forest models successfully distinguished unhealthy gut samples from healthy samples through the key competitive and cooperative microbiota, suggesting potential links between community metabolic interactions and host health. Together, this study enhances our mechanistic understanding of microbial interaction dynamism within complex gut ecosystems, offering new targets for understanding host health.}, } @article {pmid41130504, year = {2026}, author = {Song, Y and Zhang, J and Shen, X and Yang, L and Jia, Y and Song, F and Huang, Y and Han, B and Zhang, N and Ma, G}, title = {Study on the association between microplastic exposure and gut microbiota based on metagenomics: A pilot study on 66 young college students in China.}, journal = {Environmental research}, volume = {288}, number = {Pt 1}, pages = {122995}, doi = {10.1016/j.envres.2025.122995}, pmid = {41130504}, issn = {1096-0953}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Microplastics/analysis ; Pilot Projects ; Metagenomics ; Female ; Male ; Young Adult ; China ; Feces/chemistry/microbiology ; *Environmental Exposure ; Students ; *Environmental Pollutants/analysis ; Adolescent ; Bacteria ; Adult ; }, abstract = {OBJECTIVE: This study aimed to evaluate the types and mass concentrations of microplastics found in the stools of young college students. The underlying connections between microplastic exposure and gut microbiota were revealed.

METHODS: The study involved 66 participants, from whom stool samples were collected. Pyrolysis gas chromatography/mass spectrometry (Py-GCMS) was used to identify the types and mass concentrations of microplastics. Metagenomic sequencing was performed on the gut microbiota using high-throughput sequencing and metagenomic analysis techniques. Participants were divided into low group (LG) and high group (HG) based on the median mass concentration of microplastics in their stools. The differences in microbial diversity and species with significant differences between the two groups were analyzed. Spearman's correlation analysis was conducted to assess the associations between microbial characteristics and gene functions.

RESULTS: The detection rate of microplastics in the stool samples was 98.5 %, with a median mass concentration of 54.7 μg/g. Significant differences were observed in gut microbiota between the two groups in terms of alpha and beta diversities. The relative abundance of Segatella copri was higher in the LG, while the relative abundance of Escherichia coli was higher in the HG. Compared with the LG, the gut microbiota in the HG exhibited an increase in the relative abundance of harmful bacteria, such as Dialister invisus, Clostridium fessum, and Evtepia gabavorous. The ADONIS analysis revealed that PS microplastics had a significant impact on the structure of the gut microbiota. However, no significant differences were observed among the metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes database between the two groups at either level I or II.

CONCLUSION: Participants with higher mass concentrations of microplastics in their stools exhibited an increase in the abundance of harmful intestinal bacteria. PS microplastics had the most profound impact on the gut microbiota structure.}, } @article {pmid40902348, year = {2025}, author = {Zhou, N and Gu, T and Duan, M and Tian, Y and Chen, L and Zeng, T and Hou, X and Wang, X and Xu, Q and Zhang, Y and Lu, L}, title = {Gut microbiota dysbiosis exacerbates polystyrene microplastics-induced liver inflammation via activating LPS/TLR4 signaling pathway in ducks.}, journal = {Poultry science}, volume = {104}, number = {11}, pages = {105757}, pmid = {40902348}, issn = {1525-3171}, mesh = {Animals ; *Ducks ; *Microplastics/toxicity/adverse effects ; Signal Transduction/drug effects ; *Gastrointestinal Microbiome/drug effects ; Toll-Like Receptor 4/metabolism/genetics ; *Polystyrenes/toxicity/adverse effects ; Lipopolysaccharides/metabolism ; *Dysbiosis/veterinary/chemically induced ; *Poultry Diseases/chemically induced/microbiology ; Liver/drug effects ; *Inflammation/veterinary/chemically induced ; Avian Proteins/metabolism/genetics ; }, abstract = {Ubiquitous microplastics can bioaccumulate in organisms, resulting in detrimental health impacts, such as liver inflammation. Nonetheless, the exact mechanism by which polystyrene microplastics (PS-MPs) trigger liver inflammation via the gut-liver axis in ducks remains unclear. The purpose of this study was to clarify the impact of PS-MPs exposure to liver inflammation through the gut-liver axis in ducks. Our investigation indicated that exposure to PS-MPs markedly upregulated the levels of MDA and ROS in the liver tissue and enhanced the release of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β). Additionally, PS-MPs exposure increased the LPS level, which ultimately triggered the TLR4/NF-κB signaling pathway. Notably, exposure to PS-MPs resulted in a marked change in the gut microbiota composition, primarily indicated by an increase in the relative abundance of Brachyspiraceae and a reduction in that of CAG-74 and Oscillospiraceae. Metabolome analysis further revealed that different expressed metabolites (DEMs) in the positive and negative mode were identified between the control and HMPs groups, including 1-methylhistamine, DL-Methionine sulfoxide, Guanidinoethyl sulfonate, l-Cysteic acid, Deoxyinosine, Camp. Both metagenomic and metabolome analyses showed enrichment in the lysosomal pathway. Correlation analysis suggested association among representative gut microbiota, serum LPS, oxidative stress factors, liver DEMs and key liver inflammatory indicators. Our study sheds light on the mechanism by which PS-MPs exposure induced liver inflammation in ducks via the modulation of the gut-liver axis. These findings improved our understanding of the underlying mechanisms that contribute to PS-MPs-induced hepatotoxicity in avian species.}, } @article {pmid41315266, year = {2025}, author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P}, title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10777}, pmid = {41315266}, issn = {2041-1723}, support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Zea mays/microbiology/genetics/growth & development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; }, abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.}, } @article {pmid41315190, year = {2025}, author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and , and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M}, title = {Unveiling the global urban virome through wastewater metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10707}, pmid = {41315190}, issn = {2041-1723}, support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; }, mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; Cities ; Animals ; Metagenome ; }, abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.}, } @article {pmid41312645, year = {2025}, author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC}, title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1283}, pmid = {41312645}, issn = {1362-4962}, support = {DE-AC02-05CH11231//US DOE/ ; FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Hellenic Foundation for Research and Innovation/ ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; }, abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.}, } @article {pmid41312302, year = {2025}, author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {450}, pmid = {41312302}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).}, } @article {pmid41312195, year = {2025}, author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W}, title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {5191656}, pmid = {41312195}, issn = {1865-1682}, mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; }, abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.}, } @article {pmid41310806, year = {2025}, author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J}, title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {248}, pmid = {41310806}, issn = {2049-2618}, support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; }, abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.

RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.

CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.}, } @article {pmid41310797, year = {2025}, author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X}, title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.}, journal = {Radiation oncology (London, England)}, volume = {20}, number = {1}, pages = {179}, pmid = {41310797}, issn = {1748-717X}, support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; }, mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; }, abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.

METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72 h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.

RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p < 0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4 + T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5⁺ intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.

CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.}, } @article {pmid41310780, year = {2025}, author = {Liu, Y and Brinkhoff, T and Simon, M}, title = {Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {247}, pmid = {41310780}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Roseobacter/genetics/classification/isolation & purification ; Phylogeny ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; Phylogeography ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA ; Genome, Bacterial ; }, abstract = {BACKGROUND: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.

RESULTS: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for ~ 70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of < 2.9 Mbp and G + C contents of < 40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.

CONCLUSIONS: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.}, } @article {pmid41309890, year = {2025}, author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E}, title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42423}, pmid = {41309890}, issn = {2045-2322}, support = {100217/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; }, abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.}, } @article {pmid41309379, year = {2025}, author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH}, title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2506014}, doi = {10.4014/jmb.2506.06014}, pmid = {41309379}, issn = {1738-8872}, mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Streptococcus/metabolism ; }, abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.}, } @article {pmid41299763, year = {2025}, author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N}, title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {243}, pmid = {41299763}, issn = {2049-2618}, support = {Fondecyt 1230758//Agencia Nacional de Investigación y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; }, mesh = {*Gene Transfer, Horizontal ; Animals ; Antarctic Regions ; *Microbiota/genetics ; *Porifera/microbiology/physiology ; Cold Temperature ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; *Adaptation, Physiological/genetics ; Seawater/microbiology ; Phylogeny ; Acclimatization ; }, abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.

RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.

CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.}, } @article {pmid40768327, year = {2025}, author = {Gilbert, E and Binks, S and Damato, V and Uy, C and Colmenero, P and Kelly, M and Khalil, MI and O'Brien, M and Claesson, MJ and Cryan, JF and Delanty, N and Irani, SR and Cavalleri, GL}, title = {The gut microbiome associated with LGI1-antibody encephalitis.}, journal = {Epilepsia}, volume = {66}, number = {11}, pages = {4411-4424}, doi = {10.1111/epi.18556}, pmid = {40768327}, issn = {1528-1167}, support = {MRCG-2018-005//Medical Research Charities Group/ ; 104079/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 16/RC/3948/SFI_/Science Foundation Ireland/Ireland ; MR/V007173/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Female ; Male ; *Intracellular Signaling Peptides and Proteins/immunology ; *Encephalitis/immunology/microbiology/genetics ; *Autoantibodies/immunology ; Adult ; Middle Aged ; Young Adult ; Aged ; }, abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.

METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls, and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.

RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.

SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.}, } @article {pmid41307726, year = {2025}, author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM}, title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-025-02595-0}, pmid = {41307726}, issn = {1432-184X}, support = {88887-468244-2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovación/ ; Serra-1709-17818//Instituto Serrapilheira/ ; }, abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.}, } @article {pmid41306589, year = {2025}, author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H}, title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1708266}, pmid = {41306589}, issn = {2235-2988}, mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation & purification ; *Murinae/microbiology ; }, abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.

METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.

RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.

CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.}, } @article {pmid41305578, year = {2025}, author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V}, title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.}, journal = {Nutrients}, volume = {17}, number = {22}, pages = {}, doi = {10.3390/nu17223527}, pmid = {41305578}, issn = {2072-6643}, support = {469073465//DFG/ ; }, mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; }, abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.}, } @article {pmid41305529, year = {2025}, author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W}, title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.}, journal = {Viruses}, volume = {17}, number = {11}, pages = {}, doi = {10.3390/v17111508}, pmid = {41305529}, issn = {1999-4915}, support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; }, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; }, abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.}, } @article {pmid41305373, year = {2025}, author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH}, title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/pathogens14111136}, pmid = {41305373}, issn = {2076-0817}, support = {ĐTĐLCN.63/22//Ministry of Science and Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation & purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; }, abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.}, } @article {pmid41304309, year = {2025}, author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN}, title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.}, journal = {Microorganisms}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/microorganisms13112625}, pmid = {41304309}, issn = {2076-2607}, support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; }, abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.}, } @article {pmid41299634, year = {2025}, author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V}, title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {241}, pmid = {41299634}, issn = {2049-2618}, support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; }, abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.

RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.

CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.}, } @article {pmid41299624, year = {2025}, author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W}, title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {242}, pmid = {41299624}, issn = {2049-2618}, support = {81825019//National Science Fund for Distinguished Young Scholars/ ; }, mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.

RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.

CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.}, } @article {pmid41299512, year = {2025}, author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B}, title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.}, journal = {Reproductive biology and endocrinology : RB&E}, volume = {23}, number = {1}, pages = {154}, pmid = {41299512}, issn = {1477-7827}, mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation & purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; }, abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.

METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n = 15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n = 13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.

RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p = 0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.

CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.}, } @article {pmid41298564, year = {2025}, author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP}, title = {Laser-assisted microbial culturomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10614}, pmid = {41298564}, issn = {2041-1723}, support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Biofilms/growth & development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification/growth & development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; }, abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.}, } @article {pmid41298409, year = {2025}, author = {Thorpe, AC and Busi, SB and Warren, J and Hunt, LH and Walsh, K and Read, DS}, title = {National-scale biogeography and function of river and stream bacterial biofilm communities.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10571}, pmid = {41298409}, issn = {2041-1723}, support = {SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/X011089/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Biofilms/growth & development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; England ; Ecosystem ; Biodiversity ; Metagenomics ; Metagenome ; Microbiota/genetics ; Phylogeny ; }, abstract = {Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England's extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.}, } @article {pmid41298355, year = {2025}, author = {Holcik, L and von Haeseler, A and Pflug, FG}, title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10523}, pmid = {41298355}, issn = {2041-1723}, mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; }, abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.}, } @article {pmid41148242, year = {2025}, author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R}, title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {72}, number = {4}, pages = {296-312}, doi = {10.1556/030.2025.02725}, pmid = {41148242}, issn = {1588-2640}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases/diagnosis/microbiology ; *Artificial Intelligence ; Machine Learning ; Dysbiosis ; }, abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.}, } @article {pmid41118252, year = {2025}, author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z}, title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {72}, number = {4}, pages = {287-295}, doi = {10.1556/030.2025.02690}, pmid = {41118252}, issn = {1588-2640}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diarrhea/chemically induced/therapy/microbiology ; *Anti-Bacterial Agents/adverse effects ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Dysbiosis/chemically induced/therapy ; Animals ; }, abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.}, } @article {pmid40783881, year = {2025}, author = {Maldonado-Gómez, JC and Rincón-Molina, FA and Rincón-Rosales, R and Manzano-Gómez, LA and Gen-Jiménez, A and Rincón-Molina, CI}, title = {Diversity and plant growth-promoting properties of rhizospheric and endophytic bacteria associated with Agave americana.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {4}, pages = {2777-2790}, pmid = {40783881}, issn = {1678-4405}, support = {21914.25-P//Tecnológico Nacional de México/ ; 22004.25-P//Tecnológico Nacional de México/ ; }, mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; *Endophytes/classification/genetics/isolation & purification/metabolism ; *Agave/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; Biodiversity ; Indoleacetic Acids/metabolism ; Plant Growth Regulators/metabolism ; Phylogeny ; Plant Roots/microbiology/growth & development ; Plant Development ; }, abstract = {Plant-microbe interactions play a critical role in maintaining plant health, enhancing soil fertility, and sustaining ecosystem functionality. Agave americana (Asparagales, Asparagaceae, L.), a crassulacean acid metabolism (CAM) species known for its remarkable drought tolerance and diverse industrial uses, represents a valuable model for exploring the ecological and functional dynamics of these associations. This study explores the diversity and functional potential of bacterial communities associated with A. americana and their role in promoting plant growth. A combination of culture-dependent techniques and metagenomic sequencing was employed to isolate and characterize rhizospheric and endophytic bacteria. Prominent bacterial genera identified included Acinetobacter, Bacillus, Rhizobium/Mesorhizobium, and Microbacterium. Metagenomic analyses revealed a high abundance of Actinobacteria, Proteobacteria, and Chloroflexi, highlighting their roles in nutrient cycling and organic matter decomposition. Plant growth-promoting assays demonstrated that Rhizobium sp. 34 A produced significant levels of indole-3-acetic acid (IAA), enhancing nutrient availability and plant growth. Mesorhizobium sp. 28 A had the greatest overall impact, significantly increasing total fresh weight, chlorophyll content, and sugar profiles, surpassing the effects of chemical fertilizers. Furthermore, Bacillus sp. T12C12, in combination with other plant growth-promoting bacteria (PGPB), exhibited the highest nitrogenase activity, as measured through acetylene reduction assays (ARA). These findings suggest that bacterial inoculants can enhance the nutritional and agronomic value of Agave species, which are of significant agro-industrial and food importance, providing a sustainable alternative to chemical fertilizers. This study offers valuable insights into sustainable agricultural practices by leveraging microbial communities to enhance crop productivity and resilience.}, } @article {pmid41298327, year = {2025}, author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ}, title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70229}, doi = {10.1111/1758-2229.70229}, pmid = {41298327}, issn = {1758-2229}, support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; }, mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; }, abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.}, } @article {pmid41291881, year = {2025}, author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A}, title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.}, journal = {Biology of sex differences}, volume = {16}, number = {1}, pages = {101}, pmid = {41291881}, issn = {2042-6410}, support = {T32DK007180/GF/NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; R01 MD015904/GF/NIH HHS/United States ; }, mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; }, abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.

AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.

METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as ≥2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.

RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.

CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.}, } @article {pmid41290854, year = {2025}, author = {Chauhan, A and Chukwujindu, C and Pathak, A and Jaswal, R}, title = {A survey of bacterial and fungal community structure and functions in two long-term metalliferous soil habitats.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41955}, pmid = {41290854}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; *Soil Pollutants/analysis ; Mercury/analysis ; Ecosystem ; *Microbiota ; Soil/chemistry ; Metagenomics ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mercury contamination at legacy nuclear sites such as the Savannah River Site and Oak Ridge Reservation poses persistent ecological risks, yet its impact on soil microbiomes remains incompletely understood. This study integrates qPCR, 16S/ITS amplicon sequencing, and shotgun metagenomics to assess bacterial and fungal community structure, diversity, and functional potential across gradients of total mercury, methylmercury, and bioavailable mercury. Bacterial α-diversity declined with increasing Hg levels, while fungal diversity remained stable and highest in low-contamination soils. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Bacillota, Acidobacteriota, and Actinomycetota; fungal communities were primarily Ascomycota and Basidiomycota. Canonical correspondence analysis revealed distinct taxon-Hg speciation linkages, and functional gene profiling showed enrichment of stress-response genes, membrane transporters, and phosphate metabolism pathways in contaminated soils. Notably, bioavailable Hg did not correlate directly with total Hg, underscoring the importance of speciation in microbial exposure. These findings highlight the adaptive plasticity of native microbiomes and identify microbial taxa and pathways relevant to bioremediation and can guide ecosystem restoration activities in Hg-impacted soil habitats.}, } @article {pmid41290836, year = {2025}, author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS}, title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41935}, pmid = {41290836}, issn = {2045-2322}, mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.}, } @article {pmid41164876, year = {2025}, author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K}, title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {45}, number = {12}, pages = {e594-e607}, doi = {10.1161/ATVBAHA.125.322968}, pmid = {41164876}, issn = {1524-4636}, mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Plaque, Atherosclerotic ; *Carotid Artery Diseases/immunology/microbiology/diagnostic imaging/blood/genetics/epidemiology ; Biomarkers/blood ; Prospective Studies ; Aged ; China/epidemiology ; *Complement Pathway, Alternative/genetics ; *Inflammation Mediators/blood ; Mendelian Randomization Analysis ; Risk Factors ; Longitudinal Studies ; Complement C3 ; *Inflammation/blood ; }, abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.

METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age±SD, 57.75±5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3×. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.

RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (complement C3; odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.

CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.}, } @article {pmid40816543, year = {2025}, author = {Amarlapudi, MR and Balasubramaniam, C and Akash, and Singh, H and Yadav, A and Hirikyathanahalli Vishweswaraiah, R and Pradhan, D and Kumar, N and Dhotre, D and Kolte, AP and Hogarehalli Mallappa, R}, title = {Microbiome and antibiotic resistance profile of milk and faeces from cattle in an organized dairy production system.}, journal = {International journal of antimicrobial agents}, volume = {66}, number = {6}, pages = {107590}, doi = {10.1016/j.ijantimicag.2025.107590}, pmid = {40816543}, issn = {1872-7913}, mesh = {Animals ; Cattle ; *Feces/microbiology ; *Milk/microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota ; Dairying ; Metagenomics ; Metagenome ; Microbial Sensitivity Tests ; Female ; }, abstract = {Antimicrobial resistance (AMR) represents a critical public health challenge, responsible for over one million fatalities each year. Livestock, particularly dairy cattle, significantly contribute to the AMR crisis due to the extensive use of antibiotics in the animal health sector. This study aimed to characterize the antibiotic resistome of dairy cattle by analyzing their fecal and milk metagenomes. We collected 36 milk and 36 fecal samples from three different organized dairy farms and extracted metagenomic DNA, yielding 2.58 and 2.81 billion total reads contributing 200.4 and 206.5 GB data, respectively. The majority of these reads mapped to bacterial genomes, revealing 37 bacterial phyla within the dairy production system, with greater phylum-level diversity observed in feces compared to milk. The predominant phyla identified were Bacillota (53.3%), Pseudomonadota (24.7%), Bacteroidota (11.0%), and Actinomycetota (8.4%). The most abundant genera found were Clostridium in milk and Bifidobacterium in feces. In total, we identified 290 distinct antibiotic-resistant genes spanning 27 diverse drug classes and 12 resistance mechanisms. The abundance of antibiotic-resistant genes was higher in feces than in milk, with 229 distinct antibiotic-resistant genes found in milk. Overall, aminoglycoside-resistant genes were the most prevalent and abundant in both fecal and milk metagenomes of cattle from organized dairy production systems.}, } @article {pmid40622282, year = {2025}, author = {Ni, Z and Zhou, Y and Chang, M and Xia, T and Zhou, W and Gao, Y}, title = {High-Altitude Impacts on Gut Microbiota: Accelerated Aging and the Urgency for Targeted Health Interventions.}, journal = {High altitude medicine & biology}, volume = {26}, number = {4}, pages = {388-392}, doi = {10.1089/ham.2025.0016}, pmid = {40622282}, issn = {1557-8682}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Altitude ; Adult ; *Aging/physiology ; Male ; Female ; Feces/microbiology ; Middle Aged ; Young Adult ; Bacteroidetes/isolation & purification ; Aged ; Firmicutes/isolation & purification ; }, abstract = {Ni, Zhexin, Yongqiang Zhou, Mingyang Chang, Tiantian Xia, Wei Zhou, and Yue Gao. High-altitude impacts on gut microbiota: Accelerated aging and the urgency for targeted health interventions. High Alt Med Biol. 26:416-423, 2025.-The human gut microbiota is integral to the aging process, and its composition is notably influenced by the unique environmental pressures of high-altitude plateaus, characterized by hypobaric and hypoxic conditions. This study explores the correlation between physiological aging and gut microbiota among high-altitude plateau inhabitants, an essential aspect of health preservation in such regions. We conducted a metagenomic analysis of fecal samples from 105 individuals who migrated to high-altitude areas before the age of 20. Our results demonstrate that advancing age and prolonged high-altitude living significantly modify the gut microbiota, evidenced by reduced diversity and an elevated Firmicutes to Bacteroidetes (F/B) ratio in older subjects. Notably, the abundance of the anti-aging bacterium Akkermansia muciniphila (A. muciniphila) inversely correlates with age, showing a significant decline post the age of 25. A comparative analysis of 2,007 individuals from lower altitudes revealed a similar negative correlation between A. muciniphila and age, with a decline evident from age 38. These findings indicate that the high-altitude plateau environment may accelerate the decline of A. muciniphila by 10 years, underscoring the need for targeted health strategies for high-altitude populations.}, } @article {pmid41290652, year = {2025}, author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN}, title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10492}, pmid = {41290652}, issn = {2041-1723}, mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; }, abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.}, } @article {pmid41289388, year = {2025}, author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI}, title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {48}, pages = {e2523178122}, doi = {10.1073/pnas.2523178122}, pmid = {41289388}, issn = {1091-6490}, support = {DK30292//HHS | NIH (NIH)/ ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; K01DK134840/GF/NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Goblet Cells/metabolism/physiology ; *Germ-Free Life ; Female ; Humans ; *Malnutrition/microbiology ; Child ; }, abstract = {Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, "reverse translation" experiments are performed where intact fecal microbiomes collected from trial participants before and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes, and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because "no treatment" control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes in microbial gene expression consistent with a less virulent gut ecosystem and alterations in expression of i) components of cell junctions in the enterocytic and goblet cell lineages, ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.}, } @article {pmid41286929, year = {2025}, author = {Liu, J and Wang, M and Xu, C and Jia, L and Lai, S and Zhang, ZC and Zhang, J and Chen, WH and Yang, YT and Zhao, XM}, title = {HGMT: a database of human gut microbiota for tumors and immunotherapy response.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {401}, pmid = {41286929}, issn = {1474-760X}, support = {2024YFA0918500//National Key Research and Development Program of China/ ; 2023YFF1204800//National Key Research and Development Program of China/ ; 24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Immunotherapy ; *Neoplasms/therapy/microbiology ; Metagenomics ; }, abstract = {HGMT is a database designed to analyze, explore, and visualize gut microbiomes from diverse tumor types. We process metagenomic datasets from 18,630 stool samples across 37 tumor types, including 2,207 samples from immunotherapy-treated patients across 12 tumor types. HGMT provides an interactive portal for querying taxonomic and functional profiles, visualizing cross-dataset differential abundance taxa in tumors, and identifying their pan-tumor associations. Our analysis reveals the capability of gut microbiota in diagnosing gastrointestinal tumors and predicting immunotherapy response for non-small cell lung carcinoma. HGMT represents a valuable resource for investigating the roles of gut microbiota in tumors and immunotherapy response.}, } @article {pmid41286799, year = {2025}, author = {Lawrence, K and Fibert, P and Toribio-Mateas, M and Gregory, AM and Hobbs, J and Quadt, F and Wright, S and Cotter, PD and Patel, S and Myrissa, K}, title = {Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.}, journal = {BMC psychiatry}, volume = {25}, number = {1}, pages = {1117}, pmid = {41286799}, issn = {1471-244X}, mesh = {Humans ; Child ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Double-Blind Method ; Adolescent ; *Kefir ; *Sleep ; Attention ; Severity of Illness Index ; }, abstract = {BACKGROUND: Evidence indicates the gut microbiome may be altered in ADHD, suggesting that targeting gut bacteria could alleviate symptoms. This study examined the effects of kefir supplementation on ADHD symptoms, sleep, attention, and gut microbiome composition in children diagnosed with ADHD.

METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13 years with ADHD. Participants were assigned either to a daily kefir or placebo drink group. The primary outcome was ADHD symptom severity measured by the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scale. Secondary outcomes included gut microbiota composition (analysed using shotgun metagenomic sequencing), gastrointestinal symptoms, sleep (actigraphy, parent/self-report), attention and impulsivity.

RESULTS: Fifty-three participants (mean age = 10.2 years, SD = 1.7) completed the study. Kefir had no significant overall effect on parent or teacher-rated ADHD symptom severity. A non-significant interaction was observed between baseline symptom severity and group for teacher-rated SWAN scores, with children in the kefir group who had the highest baseline ADHD symptoms showing lower scores at week six (M = 2.03, SE = 0.33 vs. 2.86, SE = 0.34), p = 0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M = 70.10, SE = 0.09) than the placebo group (M = 89.72, SE = 0.07), p = 0.04. However, the kefir group self-reported more sleep problems post-intervention (M = 39.81, SE = 0.75 vs. 37.40, SE = 0.65), p = 0.02. For Go/NoGo RT variance, a non-significant interaction (p = 0.052) between baseline and post intervention scores was found. No other significant group differences were observed. Kefir supplementation did not significantly affect gut microbiota alpha or beta diversity. However, relative abundance of several species including bifidobacterium adolescentis, B. infantis, and B. longum and Alistipes sp021204515 and A. timonensi increased significantly in the kefir group.

CONCLUSIONS: Kefir supplementation may support modest improvements in sleep quality, in children with ADHD. These findings contribute to our understanding of the potential role of nutrition in ADHD management and may inform clinical guidance for practitioners working with neurodivergent individuals.

ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.

TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.}, } @article {pmid41285810, year = {2025}, author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Saenz, CN and Zimmern, PE and Shulaev, V and De Nisco, NJ}, title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {216}, pmid = {41285810}, issn = {2055-5008}, support = {F32DK128975/NH/NIH HHS/United States ; R01DK131267/NH/NIH HHS/United States ; }, mesh = {Humans ; *Urinary Tract Infections/microbiology/urine/diagnosis ; Female ; *Microbiota ; Biomarkers/urine ; Recurrence ; Metabolomics ; *Urinary Tract/microbiology ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Urine/microbiology/chemistry ; Adult ; Middle Aged ; Deoxycholic Acid/urine ; }, abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge, and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the urinary microbiota engages with the biochemical environment of the urogenital tract is yet to be fully defined. Here, we leverage paired metagenomic and quantitative metabolomic data to establish a microbe-metabolite association network of the female urinary microbiome and define metabolic signatures of rUTI. We observe unique metabolic networks of uropathogens and uroprotective species, highlighting potential metabolite-driven ecological shifts influencing rUTI susceptibility. We find distinct metabolites associated with urinary microbiome diversity and identify a lipid signature of active rUTI that accurately distinguishes our cases from controls. Finally, we identify deoxycholic acid as a prognostic indicator for UTI recurrence. Together, these findings provide insight into microbiome-metabolite interactions within the female urinary tract and highlight potential biomarkers for the development of new diagnostic tools to improve patient outcomes.}, } @article {pmid41285752, year = {2025}, author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T}, title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10336}, pmid = {41285752}, issn = {2041-1723}, mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; }, abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.}, } @article {pmid41183495, year = {2025}, author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC}, title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish sauce.}, journal = {Letters in applied microbiology}, volume = {78}, number = {11}, pages = {}, doi = {10.1093/lambio/ovaf128}, pmid = {41183495}, issn = {1472-765X}, support = {112-2313-B-020-017-MY3//National Science and Technology Council of Taiwan/ ; NPUST-KMU-111-P009//National Pingtung University of Science and Technology/ ; }, mesh = {*Biogenic Amines/metabolism/analysis ; Fermentation ; *Enterococcaceae/metabolism/isolation & purification/genetics/classification ; *Fish Products/microbiology/analysis ; *Microbiota ; Animals ; *Fermented Foods/microbiology ; Food Microbiology ; Fishes ; Cadaverine/analysis/metabolism ; }, abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/l) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.}, } @article {pmid41114585, year = {2025}, author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T}, title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.}, journal = {mSphere}, volume = {10}, number = {11}, pages = {e0042925}, doi = {10.1128/msphere.00429-25}, pmid = {41114585}, issn = {2379-5042}, support = {R01AG079224-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Mice ; *Genotype ; Mice, Inbred C57BL ; *Apolipoproteins E/genetics ; Feces/microbiology ; Humans ; Sex Factors ; Bacteria/classification/genetics/isolation & purification ; Mice, Transgenic ; Alzheimer Disease/microbiology/genetics ; Dysbiosis/microbiology ; }, abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.}, } @article {pmid41081506, year = {2025}, author = {Jiang, C and Wu, Y and Qiu, C and Zhu, S and Zhang, Y and Shui, W}, title = {Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems.}, journal = {mSphere}, volume = {10}, number = {11}, pages = {e0034825}, doi = {10.1128/msphere.00348-25}, pmid = {41081506}, issn = {2379-5042}, support = {41871198//National Natural Science Foundation of China/ ; 42471292//National Natural Science Foundation of China/ ; XRC-23078//Fuzhou University Reaserch Start-up Project/ ; }, mesh = {*Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Archaea/genetics/classification ; *Bacteria/genetics/classification/drug effects ; Ecosystem ; Fungi/genetics/classification ; Microbiota ; Biodiversity ; Metagenome ; China ; }, abstract = {Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were Proteobacteria, Actinobacteria, and Acidobacteria; the dominant archaea were Crenarchaeota; and the dominant fungi were Ascomycota. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were CeoB, AcrB, and MexF. Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems. IMPORTANCE Currently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.}, } @article {pmid41282988, year = {2025}, author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y}, title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20199}, pmid = {41282988}, issn = {2167-8359}, mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Archaea/genetics/isolation & purification ; }, abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.

METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.

RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.

CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.}, } @article {pmid41282978, year = {2025}, author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J}, title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20348}, pmid = {41282978}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; }, abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.}, } @article {pmid41278541, year = {2025}, author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T}, title = {MeTAline: enabling reproducible and scalable metagenomic analyses.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf158}, pmid = {41278541}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; }, abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.}, } @article {pmid41278154, year = {2025}, author = {Zheng, L and Duan, SL and Wang, K}, title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.}, journal = {World journal of gastroenterology}, volume = {31}, number = {42}, pages = {113170}, pmid = {41278154}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; }, abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.}, } @article {pmid41271709, year = {2025}, author = {Bay, SK and Ni, G and Lappan, R and Leung, PM and Wong, WW and Ry Holland, SI and Athukorala, N and Knudsen, KS and Fan, Z and Kerou, M and Jain, S and Schmidt, O and Eate, V and Clarke, DA and Jirapanjawat, T and Tveit, A and Featonby, T and White, S and White, N and McGeoch, MA and Singleton, CM and Cook, PLM and Chown, SL and Greening, C}, title = {Microbial aerotrophy enables continuous primary production in diverse cave ecosystems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10295}, pmid = {41271709}, issn = {2041-1723}, mesh = {*Caves/microbiology ; *Ecosystem ; Carbon Dioxide/metabolism ; Metagenome ; Geologic Sediments/microbiology ; Microbiota/genetics ; Hydrogen/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; Biodiversity ; Carbon Monoxide/metabolism ; Biofilms ; Gammaproteobacteria/genetics/metabolism ; }, abstract = {Aerated caves receive minimal light energy, yet host diverse microbial communities and the strategies allowing them to meet energy and carbon needs remain unclear. We determined the processes and mediators of primary production in aerated limestone and basalt caves through paired metagenomic and biogeochemical profiling. Four caves were sampled, including sediments and biofilms, yielding 94 metagenomes. Based on 1458 metagenome-assembled genomes, over half of microbial cells encode enzymes to use atmospheric trace gases as energy and carbon sources. The most abundant microbes are chemosynthetic primary producers, notably the gammaproteobacterial methanotrophic order Ca. Methylocavales and two uncultivated actinobacterial genera predicted to grow on atmospheric hydrogen, carbon dioxide, and carbon monoxide. Biogeochemical and isotopic measurements confirmed that these gases are rapidly consumed at rates likely sustaining a substantial fraction of the community and potentially driving primary production. Conventional chemolithoautotrophs, using ammonium and sulfide, are also enriched and active. Altogether, these results indicate that caves are unique in microbial biodiversity and the biogeochemical processes sustaining them. Consumption of atmospheric trace gases likely has a dual role in caves, providing energy for microbial survival and potentially supporting chemosynthetic growth, thereby introducing organic carbon. This process, defined as 'aerotrophy', operates alongside organic and inorganic inputs.}, } @article {pmid41269405, year = {2025}, author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q}, title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.}, journal = {Clinical reviews in allergy & immunology}, volume = {68}, number = {1}, pages = {102}, pmid = {41269405}, issn = {1559-0267}, support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; }, mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; }, abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.}, } @article {pmid41182235, year = {2025}, author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E}, title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf247}, pmid = {41182235}, issn = {1751-7370}, support = {12T5622N//FWO/ ; G092619N//FWO/ ; }, mesh = {*Daphnia/microbiology/genetics/physiology ; Animals ; *Epigenesis, Genetic ; *Cyanobacteria/physiology ; DNA Methylation ; *Host Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Stress, Physiological ; Daphnia magna ; }, abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or nontoxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed nontoxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on nontoxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.}, } @article {pmid40467492, year = {2025}, author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y}, title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.}, journal = {Circulation journal : official journal of the Japanese Circulation Society}, volume = {89}, number = {12}, pages = {1931-1939}, doi = {10.1253/circj.CJ-24-0872}, pmid = {40467492}, issn = {1347-4820}, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; Middle Aged ; *Stroke/microbiology/mortality ; *Streptococcus anginosus/isolation & purification ; Prognosis ; Saliva/microbiology ; *Dysbiosis/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.

METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.}, } @article {pmid41138869, year = {2025}, author = {Bamigbade, GB and Subhash, A and Jarusheh, H and Liu, SQ and Palmisano, G and Ayyash, M}, title = {Selenium nanoparticles stabilized by date pulp polysaccharides: Bioactivities, gut microbiota modulation and short chain fatty acids production.}, journal = {International journal of biological macromolecules}, volume = {332}, number = {Pt 2}, pages = {148387}, doi = {10.1016/j.ijbiomac.2025.148387}, pmid = {41138869}, issn = {1879-0003}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/chemistry/pharmacology ; Humans ; *Fatty Acids, Volatile/biosynthesis ; *Selenium/chemistry/pharmacology ; *Nanoparticles/chemistry ; Antioxidants/pharmacology/chemistry ; Caco-2 Cells ; Prebiotics ; }, abstract = {Natural polysaccharides confer various physiological functions, including prebiotic qualities, modulation of gut microbiota, and regulation of gut health. This study investigated the green synthesis and characterization of bioactive selenium nanoparticles synthesized from complexation of date pulp residues polysaccharides and sodium selenite (UP-SeNPs). UP-SeNPs were evaluated for in vitro bioactivities, digestion, prebiotic properties, and gut microbiota modulation. Structural analysis indicated UP-SeNPs were crystalline, spherical, evenly distributed (size 91.1 ± 2.34 nm, polydispersity index 0.071, zeta potential -25.24 mV). Compared to controls, UP-SeNPs showed significant dose-dependent radical scavenging activities: 66.8 ± 10.49 % (DPPH), 82.8 ± 1.92 % (ABTS), 495.2 ± 8.94 μg/mL (FRAP), and 981.8 ± 9.09 μg/mL (TAC) at 100 mg/L. Inhibition rates of 82.54 %, 52.97 %, and 39.84 % against α-amylase, α-glucosidase, and ACE, respectively, were noted at 100 mg/L. UP-SeNPs (50 mg/L) showed antiproliferative activities of 34.72 % against Caco-2 and 15.16 % against MCF-7. At 100 mg/L, UP-SeNPs exhibited antibacterial properties against four foodborne pathogens. UP-SeNPs supported the proliferation of standard probiotic strains, evidenced by the high Vmax, reduced lag, and extended exponential phases. Metagenomic analysis indicated that Bifidobacterium adolescentis and other species were abundant. In contrast, metabolomic analysis confirmed pathways for the synthesis of short-chain fatty acids (SCFAs), lipids, carbohydrates, amino acids, and vitamins. These findings may offer a basis for the nanobiotechnological and nanomedical applications of UP-SeNPs.}, } @article {pmid41138860, year = {2025}, author = {Mishra, S and Vadakkethil, AA and Iquebal, MA and Jaiswal, S and Kumar, D and Singh, BP and Ajlouni, S and Ranadheera, CS and Chakkaravarthi, S}, title = {Deciphering microbial diversity and predicting metabolic functionalities in fermented pigmented rice water using culture-independent characterization.}, journal = {Journal of microbiological methods}, volume = {239}, number = {}, pages = {107295}, doi = {10.1016/j.mimet.2025.107295}, pmid = {41138860}, issn = {1872-8359}, mesh = {*Oryza/microbiology/chemistry ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fungi/classification/genetics/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Food Microbiology ; Biodiversity ; *Fermented Foods/microbiology ; Phylogeny ; }, abstract = {Fermented rice water is gaining importance lately due to its traditional food culture and potential beneficial effects. Flavored fermented rice water (FFRW) produced from pigmented rice varieties, viz., black, brown, and red, is shown to have rich nutritional and functional profiles. However, the microbiota in this spontaneously fermented beverage is scantly known. Hence, this study aimed to explore the total bacterial and fungal diversity using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, respectively, along with the phytochemicals and their metabolites produced/utilized during storage. The bacterial diversity showed significant differences (p < 0.05) in black FFRW while depicting stability for brown- and red-FFRW on the 0th day and 30th day of refrigerated storage. Lactic acid bacteria (LAB) like Weissella were abundantly recorded; similarly, fungal diversity showed dominance of various yeasts. Predictive functional/metabolic pathways suggested 23 pathways of which the predominant were metabolism amino acids like branched-chain amino acids (BCAAs) viz., leucine, valine, and isoleucine, aromatic amino acids such as tryptophan, and metabolites of glycan biosynthesis, polyphenols, lipids, cofactors and vitamins. KEGG pathways revealed a shift in microbial metabolism from amino acid degradation pathways dominating on day 0 to carbohydrate and fatty acid metabolism by day 30. Enzymes like lactate dehydrogenase showed increased abundance by the 30th day, particularly in red and black-FFRW. The untargeted profiling showed that brown FFRW had more polyphenol-related compounds, followed by black and red FFRW. Decrements in the compounds were detected on the 30th day of storage compared to the 0th day. The findings provide insights into the microbial diversity, metabolic potential, and phytochemical composition of FFRW, supporting its potential as a functional beverage.}, } @article {pmid41110780, year = {2025}, author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V}, title = {Forensic application of metagenomics: Methods and future directions.}, journal = {Journal of microbiological methods}, volume = {239}, number = {}, pages = {107300}, doi = {10.1016/j.mimet.2025.107300}, pmid = {41110780}, issn = {1872-8359}, mesh = {*Metagenomics/methods/trends ; Humans ; *Microbiota/genetics ; *Forensic Sciences/methods ; Bacteria/genetics/classification/isolation & purification ; *Forensic Genetics/methods ; }, abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.}, } @article {pmid41177025, year = {2025}, author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S}, title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140254}, doi = {10.1016/j.jhazmat.2025.140254}, pmid = {41177025}, issn = {1873-3336}, mesh = {Animals ; *Benzhydryl Compounds/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Phenols/toxicity ; Mice ; Male ; *Cognition/drug effects ; Brain/drug effects/metabolism ; Maze Learning/drug effects ; *Cognitive Dysfunction/chemically induced ; Behavior, Animal/drug effects ; Dysbiosis ; Bisphenol A Compounds ; }, abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.}, } @article {pmid41175752, year = {2025}, author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H}, title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140318}, doi = {10.1016/j.jhazmat.2025.140318}, pmid = {41175752}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Heterocyclic Compounds/toxicity ; *Soil Pollutants/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Virulence Factors/genetics ; }, abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.}, } @article {pmid41172852, year = {2025}, author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S}, title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140283}, doi = {10.1016/j.jhazmat.2025.140283}, pmid = {41172852}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Female ; *Animal Feed ; Rumen/microbiology ; Feces/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.}, } @article {pmid41135463, year = {2025}, author = {Zhang, A and Pan, P and Zhou, NY and Li, T}, title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140176}, doi = {10.1016/j.jhazmat.2025.140176}, pmid = {41135463}, issn = {1873-3336}, mesh = {*Benzophenones/metabolism ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Wastewater/microbiology ; *Sunscreening Agents/metabolism ; *Microbial Consortia ; Bacteria/metabolism/genetics ; }, abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.}, } @article {pmid41130000, year = {2025}, author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z}, title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140201}, doi = {10.1016/j.jhazmat.2025.140201}, pmid = {41130000}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects/genetics ; Trimethoprim/pharmacology ; Nitrogen/metabolism ; Lincomycin/pharmacology ; Carbon/metabolism ; *Genes, Bacterial ; Sulfur/metabolism ; Drug Resistance, Microbial/genetics ; *Water Microbiology ; *Bacteria/genetics/drug effects/metabolism ; }, abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.}, } @article {pmid41110291, year = {2025}, author = {Liu, C and Liu, Y and Li, Y and Liu, M and Lu, H and Liu, X and Lu, M}, title = {Host-dominated oxidative cascades and transgenerational Cu transfer drive population collapse in Spodoptera frugiperda under chronic CuO nanoparticle exposure: Implications for nano-pesticide environmental risk assessment.}, journal = {Environment international}, volume = {205}, number = {}, pages = {109874}, doi = {10.1016/j.envint.2025.109874}, pmid = {41110291}, issn = {1873-6750}, mesh = {Animals ; *Copper/toxicity ; *Spodoptera/physiology/drug effects ; Risk Assessment ; *Metal Nanoparticles/toxicity ; Oxidative Stress/drug effects ; Gastrointestinal Microbiome/drug effects ; Nanoparticles/toxicity ; }, abstract = {The increasing use of CuO nanoparticles (NPs) in agriculture raises urgent concerns about their long-term ecological risks, particularly regarding transgenerational reproduction and gut microbiota in pest species. Here, we chronically exposed Spodoptera frugiperda to a sublethal concentration of CuO NPs (25 mg/kg). Population collapse occurred in the F4 generation (0 % survival), driven by pronounced oxidative stress (CAT and MDA activities increased up to 2.0-fold), substantial Cu accumulation in eggs (12 → 30 ng/mg) and gut tissue (25 → 750 ng/mg), and impaired reproductive output (33 % reduction in egg production with only 30 % hatching in F3). Although gut microbial diversity remained structurally stable (Shannon index, P > 0.05), metagenomic analysis revealed functional reprogramming, particularly in energy metabolism. Sterile larva inoculation assays confirmed that microbiota exacerbated toxicity, though direct NPs effects dominated. These findings highlight that current risk assessment frameworks, which are primarily focused on acute toxicity and microbial composition, severely underestimate the hazards of nanopesticides. We advocate for integrating multigenerational toxicity testing and metagenomic profiling into nano-pesticide risk evaluations to better capture population-level outcomes.}, } @article {pmid41105996, year = {2025}, author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG}, title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140144}, doi = {10.1016/j.jhazmat.2025.140144}, pmid = {41105996}, issn = {1873-3336}, mesh = {Animals ; Chickens ; *Air Microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Farms ; *DNA/analysis ; Bacteria/genetics ; Metagenomics ; }, abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.}, } @article {pmid41086989, year = {2026}, author = {Zheng, L and Yao, L and Zhu, B and Chen, S and Qian, J and Liu, S and Zhao, J and Chen, Z and Xiang, S and Xie, Z and Zhu, J and Wang, S and Wu, K and Chen, J and Zhang, S and Lu, X}, title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.}, journal = {Journal of affective disorders}, volume = {394}, number = {Pt A}, pages = {120399}, doi = {10.1016/j.jad.2025.120399}, pmid = {41086989}, issn = {1573-2517}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Adolescent ; *Bipolar Disorder/microbiology ; Male ; Female ; Child ; Phenotype ; Feces/microbiology ; Archaea/genetics ; Bacteria ; Case-Control Studies ; }, abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.}, } @article {pmid40910191, year = {2025}, author = {Yehezkel-Cortes, AM and Ruiz-Ordaz, N and Galíndez-Mayer, J and González-Juárez, S and Gómez-Murcia, V}, title = {Modeling and simulation of a modified Ludzack-Ettinger wastewater treatment bioprocess based on the concept of multifunctional microbiota.}, journal = {Environmental technology}, volume = {46}, number = {28}, pages = {5680-5694}, doi = {10.1080/09593330.2025.2551907}, pmid = {40910191}, issn = {1479-487X}, mesh = {*Wastewater/microbiology ; *Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism/analysis ; Biological Oxygen Demand Analysis ; Models, Theoretical ; Biomass ; }, abstract = {This research investigates the behavior of key components within aerobic and anoxic bioreactors in Biological Nitrogen Removal (BNR) bioprocesses. A mathematical model based on the Modified Ludzack-Ettinger (MLE) configuration is proposed. The model comprises an ensemble of ten differential equations derived from mass balances in the MLE system, complemented with a set of biokinetic models. To reduce complexity and enhance applicability, the model treats all nitrogen and phosphorus compounds as atomic N and P, and aggregates carbon sources as Chemical Oxygen Demand (COD), eliminating the need for tuning complex compound-specific parameters. The model was calibrated and validated using analytical determinations of nitrogen, phosphorus, COD, dissolved oxygen, and biomass concentrations from experiments conducted with synthetic wastewater in aerobic and anoxic reactors. Complementing this, a metagenomic study characterized the diversity and relative abundance of taxonomic groups involved in nitrogen and phosphorus metabolism within the microbial communities. Utilizing biokinetic and stoichiometric parameters for the entire microbiota, the model can be solved for both transient and steady-state conditions across a range of operational variables. It enables the estimation of bioprocess resilience following disturbances and the subsequent recovery time to a new steady state. A one-at-a-time (OAT) sensitivity analysis identified the parameters most significantly affecting state variables. The experimental results confirm the model's validity and reliability in simulating BNR processes.}, } @article {pmid40553742, year = {2025}, author = {Aharoni-Frutkoff, Y and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D}, title = {Whole Food Diet Induces Remission in Children and Young Adults With Mild to Moderate Crohn's Disease and Is More Tolerable Than Exclusive Enteral Nutrition: A Randomized Controlled Trial.}, journal = {Gastroenterology}, volume = {169}, number = {7}, pages = {1462-1474.e2}, doi = {10.1053/j.gastro.2025.06.011}, pmid = {40553742}, issn = {1528-0012}, mesh = {Humans ; *Crohn Disease/diet therapy/microbiology/diagnosis/blood/therapy ; Male ; Female ; Adolescent ; *Enteral Nutrition/adverse effects/methods ; Young Adult ; Remission Induction ; Adult ; Child ; Treatment Outcome ; Gastrointestinal Microbiome ; Severity of Illness Index ; Feces/microbiology ; Leukocyte L1 Antigen Complex/blood ; C-Reactive Protein/metabolism ; Blood Sedimentation ; Time Factors ; *Diet, Healthy/adverse effects ; }, abstract = {BACKGROUND & AIMS: Tasty&Healthy (T&H) is a whole food diet for Crohn's disease (CD) that excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized controlled trial comparing tolerability and effectiveness of T&H vs exclusive enteral nutrition (EEN).

METHODS: Patients with biologic-naïve mild to moderate CD and aged 6-25 years were randomized to either T&H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires, and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Noninvasive index, calprotectin, C-reactive protein, and erythrocyte sedimentation rate. Fecal microbiome was analyzed by metagenomics at baseline, week 4, and week 8. Data were analyzed by the intention-to-treat approach unless specified otherwise.

RESULTS: Among 83 included patients (n = 41 T&H, n = 42 EEN; mean ± SD age, 14.5 ± 3.7 years), 88% tolerated T&H vs 52% for EEN (adjusted odds ratio [aOR], 7.7; 95% CI, 2.4-25; P < .001). Calprotectin, C-reactive protein, and erythrocyte sedimentation rate decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of the T&H group vs 38% of the EEN group (aOR, 2.5; 95% CI, 0.98-6.3; P = .1; per-protocol: 67% vs 76%; P = .47). Calprotectin <250 μg/g was achieved in 34% vs 33% (aOR, 0.97; 95% CI, 0.37-2.6; P = .84) and Mucosal-Inflammation Noninvasive index score <8 in 44% vs 31% (aOR, 1.8; 95% CI, 0.7-4.5; P = .33). Microbiome α-diversity improved in the T&H arm and declined in the EEN arm, showing superior species richness at both week 4 and week 8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&H and increased in EEN (q < .001).

CONCLUSIONS: T&H demonstrated better tolerability than EEN for inducing remission in mild to moderate CD, while positively affecting the microbiome.

CLINICALTRIALS: gov, Number: NCT04239248.}, } @article {pmid41268133, year = {2025}, author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C}, title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.}, journal = {Topics in spinal cord injury rehabilitation}, volume = {31}, number = {4}, pages = {111-129}, pmid = {41268133}, issn = {1945-5763}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; }, abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.

OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).

METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).

RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.

CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.}, } @article {pmid41267624, year = {2025}, author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J}, title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70234}, doi = {10.1111/1758-2229.70234}, pmid = {41267624}, issn = {1758-2229}, support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; }, mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; }, abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.}, } @article {pmid41267035, year = {2025}, author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z}, title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {236}, pmid = {41267035}, issn = {2049-2618}, support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; }, abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.

RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.

CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.}, } @article {pmid41266796, year = {2025}, author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R}, title = {Calculating fast differential genome coverages among metagenomic sources using micov.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1624}, pmid = {41266796}, issn = {2399-3642}, mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; }, abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.}, } @article {pmid41266356, year = {2025}, author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C}, title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {215}, pmid = {41266356}, issn = {2055-5008}, support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; }, mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; }, abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.}, } @article {pmid41266326, year = {2025}, author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC}, title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10223}, pmid = {41266326}, issn = {2041-1723}, support = {1OT3HL14715//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; K01HL157658//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL157069//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL136266//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01MD011389//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; }, abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.}, } @article {pmid41151484, year = {2025}, author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J}, title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.}, journal = {International immunopharmacology}, volume = {167}, number = {}, pages = {115730}, doi = {10.1016/j.intimp.2025.115730}, pmid = {41151484}, issn = {1878-1705}, mesh = {*Melatonin/pharmacology/therapeutic use ; *NF-kappa B/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Bronchopulmonary Dysplasia/drug therapy/chemically induced/metabolism/pathology ; *Fatty Acids, Volatile/metabolism ; Mice ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Bleomycin ; Cell Line ; Lung/pathology/drug effects/metabolism ; Male ; }, abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).

METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-κB signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.

RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-κB pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-κB pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-κB activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-κB and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.

CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-κB pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.}, } @article {pmid40900671, year = {2025}, author = {Day, AS and Slater, R and Young, RB and Wheeler, RZ and Marcelino, VR and Maddigan, NK and Forster, SC and Costello, SP and Uylaki, W and Probert, CSJ and Andrews, JM and Yao, CK and Gibson, PR and Bryant, RV}, title = {Functional Profiling Demonstrates That a Sulfide-Reducing Diet Achieves Microenvironmental Targets in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {31}, number = {11}, pages = {3160-3171}, doi = {10.1093/ibd/izaf177}, pmid = {40900671}, issn = {1536-4844}, support = {//Hospital Research Foundation/ ; //University of Adelaide/ ; //Gastrointestinal Society of Australia FICE/ ; //European Crohn's Colitis/ ; //Commonwealth Research Stipend/ ; }, mesh = {Humans ; *Colitis, Ulcerative/diet therapy/metabolism/microbiology ; *Hydrogen Sulfide/metabolism ; Male ; Female ; Adult ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; *Diet ; *Sulfides/metabolism ; Volatile Organic Compounds/analysis ; }, abstract = {BACKGROUND: As a dietary approach to reducing inflammation in ulcerative colitis, the 4-SURE (4 Strategies to Sulfide Reduction) diet was designed to correct pathogenic alterations of excessive protein fermentation and hydrogen sulfide (H2S) production in the distal colon. We aimed to perform a deep functional analysis (microbial and metabolomic) of the feces of 28 adults with mild-moderately active ulcerative colitis who adhered to the 4-SURE diet over 8 weeks to explore whether the 4-SURE diet could modulate the intraluminal environment as intended.

METHODS: Fecal samples were collected at week 0 and 8 of dietary intervention, processed and aliquoted. Metagenomic sequencing was undertaken to identify changes in H2S-metabolizing genes, while gas chromatography-mass spectrometry was used to analyze fecal volatile organic compounds and H2S production.

RESULTS: The 4-SURE diet significantly increased alpha diversity between weeks 0 and 8. By random forest plot classifier, the abundance of taxonomic groups comprising known H2S-producing genera were markedly lower at week 8, specifically Odoribacter and Peptostreptococcaceae, and were of highest importance in discriminating between before- and after-diet samples. The capacity for bacterial H2S metabolism was altered with diet, with differences in 12 of 67 analyzed sulfur-metabolizing genes identified. H2S production and indole, a specific marker of protein fermentation, were significantly decreased due to the diet.

CONCLUSIONS: Here, we demonstrate that the objectives of the 4-SURE diet were fulfilled. This application of deep functional analysis to a dietary intervention study is novel and highlights an exemplar framework for including microbial and metabolomic biomarkers of pathogenic relevance in the analysis of therapeutic diet strategies. (Australian New Zealand Clinical Trials Registry, Number: ACTRN12619000063112).}, } @article {pmid40038232, year = {2025}, author = {Gohar, M and Shaheen, N and Goyal, SM and Mor, SK and Rodriguez-R, LM and Imran, M}, title = {Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {6}, pages = {5326-5344}, pmid = {40038232}, issn = {1867-1314}, support = {No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; MPC-2022-02167//OeAD-GmbH, Austria ́s Agency for Education and Internationalization/ ; No. PSF/CRP/C-QU/T-Helix (70)//Pakistan Science Foundation (PSF) Research/ ; }, mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; *Geotrichum/physiology/classification ; Mice ; Mice, Inbred BALB C ; }, abstract = {Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.}, } @article {pmid39441337, year = {2025}, author = {Shi, J and Lei, Y and Li, Z and Jia, L and He, P and Cheng, Q and Zhang, Z and Lei, Z}, title = {Alteration of Cecal Microbiota by Antimicrobial Peptides Enhances the Rational and Efficient Utilization of Nutrients in Holstein Bulls.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {6}, pages = {4491-4507}, pmid = {39441337}, issn = {1867-1314}, support = {GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; GSSLCSX-2020-1//the local funding/ ; }, mesh = {Animals ; *Cecum/microbiology/metabolism ; Cattle/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Antimicrobial Peptides/pharmacology/administration & dosage ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation & purification ; *Nutrients/metabolism ; Dietary Supplements/analysis ; }, abstract = {We previously observed that supplementation with antimicrobial peptides facilitated the average daily weight gain, net meat, and carcass weights of Holstein bulls. To expand our knowledge of the possible impact of antimicrobial peptides on cecum microbiota, further investigations were conducted. In this study, 18 castrated Holstein bulls with insignificant weight differences and 10 months of age were split randomly into two groups. The control group (CK) was fed a basic diet, whereas the antimicrobial peptide group (AP) was supplemented with 8 g of antimicrobial peptides for 270 days. After slaughter, metagenomic and metabolomic sequencing analyses were performed on the cecum contents. The results showed significantly higher levels of amylase, cellulase, protease, and lipase in the CK than in the AP group (P ≤ 0.05). The levels of β-glucosidase and xylanase (P ≤ 0.05), and acetic and propionic acids (P ≤ 0.01), were considerably elevated in the AP than in the CK group. The metagenome showed variations between the two groups only at the bacterial level, and 3258 bacteria with differences were annotated. A total of 138 differential abundant genes (P < 0.05) were identified in the CAZyme map, with 65 genes more abundant in the cecum of the AP group and 48 genes more abundant in the cecum of the CK group. Metabolomic analysis identified 68 differentially expressed metabolites. Conjoint analysis of microorganisms and metabolites revealed that Lactobacillus had the greatest impact on metabolites in the AP group and Brumimicrobium in the CK group. The advantageous strains of the AP group Firmicutes bacterium CAG:110 exhibited a strong symbiotic relationship with urodeoxycholic acid and hyodeoxycholic acid. This study identified the classification characteristics, functions, metabolites, and interactions of cecal microbiota with metabolites that contribute to host growth performance. Antimicrobial peptides affect the cecal microorganisms, making the use of nutrients more efficient. The utilization of hemicellulose in the cecum of ruminants may contribute more than cellulose to their production performance.}, } @article {pmid39313703, year = {2025}, author = {Talib, N and Mohamad, NE and Ho, CL and Masarudin, MJ and Alitheen, NB}, title = {Modulatory Effects of Isolated Lactobacillus paracasei from Malaysian Water Kefir Grains on the Intestinal Barrier and Gut Microbiota in Diabetic Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {6}, pages = {4224-4236}, pmid = {39313703}, issn = {1867-1314}, support = {FRGS/1/2017/SKK10/UPM/02/4 and FRGS-MRSA/1/2018/SKK10/UPM/02/1//Ministry of Education, Government of Malaysia./ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Kefir/microbiology ; *Lacticaseibacillus paracasei/isolation & purification/physiology ; *Probiotics/administration & dosage ; Male ; *Diabetes Mellitus, Type 2/microbiology ; Malaysia ; *Diabetes Mellitus, Experimental/microbiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {Type 2 diabetes (T2DM) is one of the four major types of non-communicable diseases that have become a global health concern. Water kefir is a product of a brown sugar solution fermented with kefir grains which comprises around 30 microbial species in its grains. Water kefir possesses a wide range of health benefits, including anti-hyperlipidemic effects, and reduces hypertension and blood glucose levels in animal models. Reportedly, consuming water kefir containing probiotics may enhance the intestinal barrier and positively influence the composition of the intestinal microflora. The present study aimed to evaluate the regulatory effects of Lactobacillus paracasei isolated from Malaysian water kefir grains (MWKG) on the alterations of intestinal barrier and gut microbiota in diabetic mice via histopathological analysis of the distal colon and 16S rRNA gene sequencing on fecal microbiome. Results indicated that the administration of isolated Lactobacillus paracasei from MWKG to diabetic mice ameliorated the dominant probiotic phyla in the gut microbiota. Results showed that lower dose (LD) and high dose (HD) treatments of the isolated Lactobacillus paracasei could significantly reduce inflammatory cell infiltration in the distal colon of diabetic mice. The treatments revealed a significant decrease in the relative abundance of Firmicutes in the gut, 0.27 ± 0.06% for LD and 0.34 ± 0.04% for HD, compared to untreated (UN) diabetic mice, 0.40 ± 0.02%. These results suggest that L. paracasei isolated from MWKG could serve as a potential dietary supplement against intestinal inflammation and modify gut microbiota composition in patients with T2DM.}, } @article {pmid41262425, year = {2025}, author = {Morelle-Hungría, E}, title = {Molecular genetics as evidence of environmental harm in ecocriminological analysis.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {244}, doi = {10.12688/openreseurope.21126.2}, pmid = {41262425}, issn = {2732-5121}, abstract = {This research focuses on the potential of molecular genetics as a tool that can complement the assessment and evaluation of environmental damage from the perspective of green criminology or ecocriminology. This would have an impact on the effectiveness and efficiency of the mechanisms established for assessing the damage caused to ecosystems. We are facing a planetary crisis with the risk of ecosystem collapse, so it is proposed to overcome the limitations that we can identify in traditional criminal law by adopting an ecocentric approach reinforced with innovative mechanisms provided by science. This requires, among other things, recognising the intrinsic value of nature and committing to ecological justice. Molecular genetics methods, such as environmental DNA, metagenomics and population genetics, allow us to visualise the biological and ecological transformations induced by pollutants, even when these are invisible to the naked eye. These techniques provide objective and quantifiable data on biodiversity loss, changes in community composition and even possible genotoxic effects. Therefore, these molecular tests can complement preventive and restorative measures in environmental crimes. By fostering dialogue between science, law, and ethics, this study advocates for an integrated paradigm of environmental damage analysis in which molecular genetics enhances our ability to detect, understand, and legally address ecological damage. The convergence of green criminology, molecular genetics, and ecological justice reorients institutional responses toward restoring ecosystem integrity and defending the rights of nature.}, } @article {pmid41261182, year = {2025}, author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S}, title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {12}, pages = {464}, pmid = {41261182}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; }, abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.}, } @article {pmid41259660, year = {2025}, author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A}, title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf620}, pmid = {41259660}, issn = {1367-4811}, abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.

RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.

raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.}, } @article {pmid41192424, year = {2025}, author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z}, title = {Assessment of enzyme diversity in the fermented food microbiome.}, journal = {Cell systems}, volume = {16}, number = {11}, pages = {101430}, doi = {10.1016/j.cels.2025.101430}, pmid = {41192424}, issn = {2405-4720}, mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Fermentation ; Food Microbiology/methods ; Metagenome/genetics ; Machine Learning ; *Enzymes/genetics/metabolism ; }, abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.}, } @article {pmid41259558, year = {2025}, author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A}, title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.}, journal = {Journal of applied oral science : revista FOB}, volume = {33}, number = {}, pages = {e20250476}, doi = {10.1590/1678-7757-2025-0476}, pmid = {41259558}, issn = {1678-7765}, mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; }, abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.

METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.

RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p≤0.05, LDA≥2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.

CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.}, } @article {pmid41258552, year = {2025}, author = {Singh, G and Tyagi, I and Tyagi, K and Kumar, V and Donthu, RK}, title = {Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {12}, pages = {1354}, pmid = {41258552}, issn = {1573-2959}, support = {core funding//Zoological Survey of India/ ; }, mesh = {*Environmental Monitoring/methods ; Public Health ; *Eukaryota/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Metagenomics ; *Metagenome ; Biodiversity ; }, abstract = {A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.}, } @article {pmid41258100, year = {2025}, author = {Wang, C and Zheng, R and Sun, C}, title = {Deep-sea viral diversity and their role in host metabolism of complex organic matter.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10134}, pmid = {41258100}, issn = {2041-1723}, mesh = {*Seawater/virology/microbiology ; *Viruses/genetics/classification/metabolism ; Virome/genetics ; Metagenomics ; Geologic Sediments/virology/microbiology ; *Host Microbial Interactions ; Genome, Viral ; Oceans and Seas ; Ecosystem ; RNA Viruses/genetics/classification ; Microbiota ; Biodiversity ; Carbon Cycle ; Transcriptome ; }, abstract = {Viruses exert a pervasive influence on biogeochemical cycles in deep-sea ecosystems. Cold seeps and seamounts, globally distributed across the oceans and harboring diverse microbial communities, remain largely unexplored regarding their viral inhabitants and functions. By integrating metagenomic, DNA viromic, RNA viromic, and metatranscriptomic data, coupled with characterization of purified viral communities, we uncover the diversity of DNA and RNA viral communities and virus-host interactions, which vary significantly across distinct deep-sea sediment sites. These sites represent a declining cold seep, a site distant from the declining cold seep (sediment site), a nascent cold seep site, and a seamount. The viral community in the nascent cold seep displays unique characteristics, with an increased proportion of RNA viruses and temperate viruses. Viral genomic and metatranscriptomic analyses reveal viral functional genes are actively expressed, potentially enhancing host metabolism of complex organic matter. Here, our findings underscore the diversity, ecological roles, and host interactions of viral communities in different cold seeps and seamounts, suggesting the importance of viruses in deep-sea carbon cycling and microbial community structure.}, } @article {pmid41255529, year = {2025}, author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L}, title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1710868}, pmid = {41255529}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; }, abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.}, } @article {pmid41250240, year = {2025}, author = {Gwak, HJ and Rho, M}, title = {DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {393}, pmid = {41250240}, issn = {1474-760X}, support = {RS-2020-II201373//the Korea government (MSIT)/ ; 20220517//Ministry of Oceans and Fisheries, Korea/ ; 2023R1A6C101A009//Korea Basic Science Institute/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Electron Transport Complex IV/genetics ; *Software ; Biodiversity ; Large Language Models ; }, abstract = {Metabarcoding remains challenging due to incomplete taxonomic annotations and computationally intensive processes. We present DeepCOI, a large language model-based classifier pre-trained on seven million cytochrome c oxidase I gene sequences. DeepCOI enables fast and accurate taxonomic assignment across eight major phyla, achieving an AU-ROC of 0.958 and AU-PR of 0.897-outperforming existing methods while significantly reducing inference time. Additionally, DeepCOI demonstrates interpretability by identifying taxonomically informative sequence positions. By integrating large-scale datasets and self-supervised learning, DeepCOI enhances both the accuracy and efficiency of metabarcoding processes, providing a scalable solution for biodiversity assessment and environmental monitoring.}, } @article {pmid41249313, year = {2025}, author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M}, title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40311}, pmid = {41249313}, issn = {2045-2322}, support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; }, abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.}, } @article {pmid41218604, year = {2025}, author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O}, title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.}, journal = {Cell reports. Medicine}, volume = {6}, number = {11}, pages = {102426}, doi = {10.1016/j.xcrm.2025.102426}, pmid = {41218604}, issn = {2666-3791}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/pharmacology/administration & dosage ; Adult ; Biomarkers/metabolism ; Young Adult ; Prednisolone/pharmacology/administration & dosage ; Healthy Volunteers ; Insulin Resistance ; Methylprednisolone/pharmacology/analogs & derivatives/administration & dosage ; Feces/microbiology ; }, abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).}, } @article {pmid41206954, year = {2025}, author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X}, title = {TCVS: tree-guided compositional variable selection analysis of microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {11}, pages = {}, doi = {10.1093/bioinformatics/btaf617}, pmid = {41206954}, issn = {1367-4811}, support = {12371287//National Natural Science Foundation of China/ ; 2022YFA1305400//National Key R&D Program of China/ ; }, mesh = {Humans ; *Microbiota ; *Software ; *Gastrointestinal Microbiome ; Algorithms ; *Computational Biology/methods ; *Metagenomics/methods ; Phylogeny ; }, abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.

RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.

TCVS R code is available at https://github.com/Yicong1225/TCVS.}, } @article {pmid41197616, year = {2025}, author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X}, title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.}, journal = {Cell reports. Medicine}, volume = {6}, number = {11}, pages = {102431}, doi = {10.1016/j.xcrm.2025.102431}, pmid = {41197616}, issn = {2666-3791}, mesh = {Humans ; *Microbiota/genetics ; *Oral Health ; *Esophageal Squamous Cell Carcinoma/microbiology ; *Esophageal Neoplasms/microbiology ; Male ; Female ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Risk Factors ; *Mouth/microbiology ; Aged ; Saliva/microbiology ; Bacteria/genetics/classification ; }, abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.}, } @article {pmid41189540, year = {2026}, author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S}, title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70066}, doi = {10.1111/1755-0998.70066}, pmid = {41189540}, issn = {1755-0998}, support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project ‛Ocean DNA'/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; }, abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.}, } @article {pmid41168956, year = {2026}, author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD}, title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70069}, doi = {10.1111/1755-0998.70069}, pmid = {41168956}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Benchmarking ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Cluster Analysis ; Biodiversity ; Computational Biology/methods ; }, abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.}, } @article {pmid41104935, year = {2025}, author = {Feijão, E and Duarte, IA and Pereira, M and Pascoal, P and Nunes, M and Tanner, SE and Dias, R and Duarte, B and Matos, AR and Figueiredo, A and Fonseca, VF}, title = {Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {11}, pages = {e0150825}, doi = {10.1128/aem.01508-25}, pmid = {41104935}, issn = {1098-5336}, support = {https://doi.org/10.54499/2022.11916.BD//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/UIDB/04292/2020, http://doi.org/10.54499/UIDP/04292/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/UIDB/04046/2020, http://doi.org/10.54499/UIDP/04046/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/UIDB/00329/2020, http://doi.org/10.54499/UIDP/00329/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/LA/P/0121/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; *Seafood/microbiology/analysis ; *Gastrointestinal Microbiome ; *Sea Bream/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Machine Learning ; Portugal ; }, abstract = {The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of Sparus aurata specimens through state-of-the-art long-read sequencing allied to machine learning tools. The gut bacteriomes of animals from four different fishing areas on the Portuguese coast were sequenced. The alpha and beta diversity analyses were shown to enable Center-South gut bacteriome differentiation from other fishing areas due to higher abundance of species of the phyla Pseudomonadota, Bacteroidota, and Bacillota and classes such as Alphaproteobacteria, Betaproteobacteria, and Bacilli. The gradient boosting machine (GBM) model selected by the H2O automatic machine learning pipeline presented a high global accuracy during training and validation phases, identifying Center-South and South sample provenance with 100% and 71.1% accuracy, respectively. By integrating the most important OTUs to the GBM model with the regional biomarkers identified through point biserial correlation analysis (indicspecies packages), a reduced set of five provenance biomarkers was identified, belonging to Gammaproteobacteria, Betaproteobacteria, and Bacilli classes, possibly highlighting the anthropogenic activities surrounding the fishing areas and local environmental abiotic factors. This study highlights the extensive and valuable information obtained by long-read sequencing and couples it with the potential of machine learning algorithms to ultimately demonstrate its efficiency in providing efficient and highly accurate seafood provenance biomarkers. This study also reports the likely influence of industrial and recreational activities, population density, and water management facilities on the gut bacteriome of S. aurata.IMPORTANCEThis study significantly contributes to a topic of utmost importance-seafood provenance analysis and seafood fraud-by leveraging gut bacteriome profiling. Through the application of long-read sequencing and machine learning, it identifies reliable biomarkers that distinguish gilthead sea bream from different fishing areas. These findings enhance traceability methods by providing a robust tool to combat seafood fraud and ensure food authenticity, thereby protecting the supply chain, the consumer, and the environment. Additionally, this study explores the possible interactions between the gut bacteriome and the industrial, recreational, and environmental factors that could influence the identified biomarkers of regional provenance while also offering insights into the composition of the marine ecosystems surrounding the fishing areas. This approach has broader implications for fishery management, sustainable sourcing, and regulatory enforcement.}, } @article {pmid41094135, year = {2025}, author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ}, title = {Isolation, engineering and ecology of temperate phages from the human gut.}, journal = {Nature}, volume = {647}, number = {8090}, pages = {698-705}, pmid = {41094135}, issn = {1476-4687}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Prophages/genetics/isolation & purification/classification/physiology ; *Bacteriophages/isolation & purification/genetics/classification/physiology ; Caco-2 Cells ; Lysogeny/genetics ; Virus Activation ; *Bacteria/virology/isolation & purification ; Genome, Viral/genetics ; }, abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.}, } @article {pmid40935888, year = {2025}, author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y}, title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.}, journal = {Journal of gastroenterology}, volume = {60}, number = {12}, pages = {1481-1495}, pmid = {40935888}, issn = {1435-5922}, support = {JP22K08040//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; Male ; Middle Aged ; Female ; *Neuroendocrine Tumors/microbiology/pathology ; *Gastrointestinal Microbiome ; *Gastric Mucosa/microbiology/pathology ; Adult ; Aged ; *Autoimmune Diseases/microbiology/pathology/complications ; *Gastritis, Atrophic/microbiology ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Stomach Neoplasms/microbiology ; Metabolome ; }, abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.

METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.

RESULTS: Microbiome analysis revealed significantly reduced α-diversity indices in patients with AIG when compared with the control group. β-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.

CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.}, } @article {pmid41249223, year = {2025}, author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL}, title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40115}, pmid = {41249223}, issn = {2045-2322}, support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; }, mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth & development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; }, abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.}, } @article {pmid41197619, year = {2025}, author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM}, title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.}, journal = {Cell reports methods}, volume = {5}, number = {11}, pages = {101218}, doi = {10.1016/j.crmeth.2025.101218}, pmid = {41197619}, issn = {2667-2375}, mesh = {Humans ; *Metagenomics/methods ; *Benchmarking/methods ; Microbiota/genetics ; Genome, Human/genetics ; *Viruses/genetics ; Polymorphism, Single Nucleotide/genetics ; Metagenome ; }, abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.}, } @article {pmid41147731, year = {2025}, author = {Jones, JA and Moczek, AP and Newton, ILG}, title = {The dung beetle microbiome complements host metabolism and nutrition.}, journal = {mSystems}, volume = {10}, number = {11}, pages = {e0117225}, doi = {10.1128/msystems.01172-25}, pmid = {41147731}, issn = {2379-5077}, support = {2243725//National Science Foundation/ ; 1901680//National Science Foundation/ ; 2141416//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; }, mesh = {Animals ; *Coleoptera/microbiology/metabolism ; *Microbiota ; Amino Acids/metabolism/biosynthesis ; Bacteria/genetics/metabolism/classification ; }, abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.}, } @article {pmid41128541, year = {2025}, author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S}, title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.}, journal = {mSystems}, volume = {10}, number = {11}, pages = {e0095625}, doi = {10.1128/msystems.00956-25}, pmid = {41128541}, issn = {2379-5077}, support = {2023YFD1702200//National Key Research and Development Program of China/ ; 42277357//National Natural Science Foundation of China/ ; 2022RC3057//Science and technology innovation Program of Hunan Province/ ; YLS-2025-ZY02039//Yuelushan Laboratory Breeding Program/ ; }, mesh = {*Composting/methods ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; Hot Temperature ; Soil Microbiology ; Metagenome ; Metagenomics ; Transcriptome ; }, abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.

IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.}, } @article {pmid41099535, year = {2025}, author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D}, title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.}, journal = {mSystems}, volume = {10}, number = {11}, pages = {e0114725}, doi = {10.1128/msystems.01147-25}, pmid = {41099535}, issn = {2379-5077}, support = {№ 0088-2024-0009//IDB RAS Government basic research program/ ; № 0088-2024-0009//IDB RAS Government basic research program/ ; }, mesh = {*Symbiosis ; Animals ; *Porifera/microbiology/physiology/classification ; *Microbiota ; Arctic Regions ; Phylogeny ; Sympatry ; Bacteria/classification/genetics ; Gammaproteobacteria/genetics/classification ; }, abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.

IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.}, } @article {pmid41055333, year = {2025}, author = {Sharma, S and Narahari, HP and Raman, K}, title = {Harnessing machine learning for metagenomic data analysis: trends and applications.}, journal = {mSystems}, volume = {10}, number = {11}, pages = {e0164224}, doi = {10.1128/msystems.01642-24}, pmid = {41055333}, issn = {2379-5077}, mesh = {*Metagenomics/methods ; *Machine Learning ; Microbiota/genetics ; Humans ; Metagenome ; }, abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.}, } @article {pmid41014671, year = {2025}, author = {Zhao, Y and Song, T and Ren, P and Wu, X and Luo, Q and Xie, J and Lai, H and Li, X and Wen, Y and Liao, X and Zhou, J}, title = {Integrating metagenomics, lipidomics and proteomics to explore the effect and mechanism of ginsenoside Rb1 on atherosclerosis co-depression disease.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {148}, number = {}, pages = {157301}, doi = {10.1016/j.phymed.2025.157301}, pmid = {41014671}, issn = {1618-095X}, mesh = {Animals ; *Ginsenosides/pharmacology ; *Atherosclerosis/drug therapy/complications ; Proteomics ; Mice ; Lipidomics ; Male ; Gastrointestinal Microbiome/drug effects ; *Depression/drug therapy/complications ; Metagenomics ; Lipid Metabolism/drug effects ; Panax/chemistry ; Mice, Inbred C57BL ; Diet, High-Fat ; Disease Models, Animal ; }, abstract = {BACKGROUND: The comorbidity of atherosclerosis (AS) and depression presents a significant clinical challenge. Its pathogenesis entails complex abnormalities in inflammatory responses, lipid metabolism, and gut microbiota homeostasis. Ginsenoside Rb1 (GRb1)-a bioactive compound derived from the dried roots of Panax ginseng (Araliaceae)-demonstrates anti-inflammatory, antioxidant, lipid-lowering, and neuroprotective properties. However, GRb1's therapeutic potential and underlying mechanisms in AS co-depression remain inadequately characterized.

PURPOSE: This study aims to elucidate the mechanism of GRb1 in AS co-depression disease, identify potential therapeutic targets, and thereby develop novel therapeutic strategies for this condition.

METHODS: An AS co-depression comorbidity model was established using ApoE[⁻/⁻] mice fed a high-fat diet and subjected to chronic restraint stress. To evaluate GRb1's therapeutic efficacy, we assessed serum lipid profiles, performed aortic Oil Red O staining, and conducted behavioral tests for depressive-like phenotypes. Furthermore, we employed an integrated multi-omics approach-combining metagenomics, targeted lipid metabolomics, and proteomics-to identify key alterations in gut microbiota, lipid metabolites, and proteins, with subsequent correlation analysis. Key differential proteins and associated pathways identified through multi-omics were validated using both in vivo (AS co-depression mouse model) and in vitro (HT22 cells) experiments. Finally, GRb1's effects on ferroptosis and specific signaling pathways (CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/GPX4) were examined via Western blotting, immunofluorescence, and transmission electron microscopy in both mouse tissues and HT22 cells.

RESULTS: Proteobacteria, Helicobacter, and Helicobacter_typhlonius represent significant intestinal microbiota components. Their primary differential lipids include phosphatidylethanolamine (PE), phosphatidylcholine (PC), and lysophosphatidylcholine (LPC), while key differential proteins encompass CD44, Gls2, and Snrpf. Notably, a strong correlation exists among Helicobacter_typhlonius, PE, and CD44. GRb1 modulates PE metabolic dysregulation by reducing the relative abundance of Helicobacter_typhlonius, thereby inhibiting lipid peroxidation and ameliorating oxidative stress. Furthermore, GRb1 suppresses the CD44/Gls2 axis, ACSL4/LPCAT3/ALOX15 pathway, and activates the SLC7A11/GPX4-mediated ferroptosis pathway, thereby exerting its anti-AS co-depression effects through these multi-target mechanisms.

CONCLUSION: GRb1 regulates the intestinal microbiota, abnormal lipid metabolism, modulates protein function, inhibits lipid peroxidation, improves oxidative stress, inhibits ferroptosis, regulates the CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/ GPX4 signaling pathways, and prevents the progression of AS co-depression disease.}, } @article {pmid41249177, year = {2025}, author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y}, title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {209}, pmid = {41249177}, issn = {2055-5008}, support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; }, abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.}, } @article {pmid41243436, year = {2025}, author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A}, title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2576657}, doi = {10.1080/19490976.2025.2576657}, pmid = {41243436}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; }, abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.}, } @article {pmid41239457, year = {2025}, author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K}, title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1287}, pmid = {41239457}, issn = {1479-5876}, mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; }, abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.

METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16 S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).

RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.

CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.}, } @article {pmid41110566, year = {2025}, author = {Wu, Z and He, Z and Dou, P and Wang, K and Zhang, Y}, title = {Study on the intestinal metabolism and absorption of polysaccharides from Dendrobium officinale.}, journal = {International journal of biological macromolecules}, volume = {331}, number = {Pt 2}, pages = {148390}, doi = {10.1016/j.ijbiomac.2025.148390}, pmid = {41110566}, issn = {1879-0003}, mesh = {*Dendrobium/chemistry ; *Polysaccharides/metabolism/chemistry/pharmacokinetics/pharmacology ; Gastrointestinal Microbiome/drug effects ; Animals ; *Intestinal Absorption ; Male ; *Intestinal Mucosa/metabolism ; Bacteroides/metabolism/genetics ; *Intestines/microbiology ; }, abstract = {Dendrobium officinale polysaccharide (DOP) is widely recognized for its excellent pharmacological activities, however, the in-depth pharmacokinetic characteristic remains unrevealed, significantly hindering its further development. It was hypothesized that Bacteroides predominantly mediates the in vivo metabolism of DOP via polysaccharide utilization loci (PULs), and the resulting oligosaccharides can be directly absorbed by the intestine. To verify this hypothesis, metagenomic sequencing analysis was first employed, confirming that DOP stimulates an upregulation of PULs associated with carbohydrate metabolism within the gut microbiota dominated by Bacteroides. The metabolized oligosaccharides were correlated with highly expressed endo-β-1,4-mannanase from Bacteroides. Further utilizing fluorescent labeling techniques, it was demonstrated that oligosaccharides derived from DOP metabolism are directly absorbed by intestinal tissues. Unabsorbed metabolites subsequently undergo disordered metabolism by gut microbiota into small molecules such as short-chain fatty acids. Collectively, these findings provide novel evidence for elucidating the pharmacological activities of DOP and offer new insights into pharmacokinetic research for other polysaccharides.}, } @article {pmid40626932, year = {2025}, author = {Talwar, C and Guria, A and Hoffman, K and Biest, S and Jimenez, P and Kommagani, R}, title = {A role for gut mycobiome and altered fungal-bacterial interactions in women with endometriosis†.}, journal = {Biology of reproduction}, volume = {113}, number = {5}, pages = {1155-1169}, doi = {10.1093/biolre/ioaf148}, pmid = {40626932}, issn = {1529-7268}, mesh = {Female ; *Endometriosis/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; *Mycobiome/physiology ; Animals ; Mice ; *Fungi/physiology ; *Bacteria ; Adult ; }, abstract = {Endometriosis is a gynecological pathology prevalent in reproductive age women in which the inner uterine wall (endometrium) grows outside as ectopic lesions. The inflammation resulting from these growing implants closely associates with disease severity, causing chronic pain and infertility. Emerging studies have found altered bacterial communities in endometriosis and a causal role for gut bacteria in endometriosis. However, the role of the gut mycobiome, i.e., the fungal component of the microbiome in endometriosis is a current knowledge gap that needs to be addressed. In this study, utilizing the stool samples from women with endometriosis, we found that the gut fungal communities are altered in women with endometriosis. By integrating the bacterial microbiota and studying the co-occurring relationships between fungi and bacteria, we identify the altered fungal-bacterial community interactions in endometriosis. In addition, we studied the microbial interactions with the host and identified the bacterial taxa as "microbiome-associated host genetic variants" in endometriosis. By determining their interactions with fungi, we highlight the fungal taxa as underlying regulators of the disease. Experimentally, we demonstrate that the progression of endometriosis in mice is significantly impeded by the depletion of fungi, revealing a role for the gut mycobiome in endometriosis. Our results highlight the positive- and negative-co-abundance relationships shared between bacteria-fungi, bacteria-bacteria, and microbes-host in the disease pathogenesis. These findings could help shape future experimental research on bacterial-fungal interactions, which should be considered when designing microbiome-based therapies that use antifungal agents.}, } @article {pmid39617895, year = {2024}, author = {Perrin, AJ and Dorrell, RG}, title = {Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {279}, pmid = {39617895}, issn = {1741-7007}, mesh = {*Climate Change ; *Eukaryota/physiology ; *Ecosystem ; Biodiversity ; }, abstract = {Eukaryotic microorganisms, or "protists," while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.}, } @article {pmid31942825, year = {2020}, author = {Ho, J and Yeoh, YK and Barua, N and Chen, Z and Lui, G and Wong, SH and Yang, X and Chan, MC and Chan, PK and Hawkey, PM and Ip, M}, title = {Systematic review of human gut resistome studies revealed variable definitions and approaches.}, journal = {Gut microbes}, volume = {12}, number = {1}, pages = {1700755}, pmid = {31942825}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/*genetics ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Humans ; }, abstract = {In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.}, } @article {pmid31226241, year = {2019}, author = {Roth, H and Gallo, S and Badger, P and Hillwig, M}, title = {Changes in microbial communities of a passive coal mine drainage bioremediation system.}, journal = {Canadian journal of microbiology}, volume = {65}, number = {10}, pages = {775-782}, doi = {10.1139/cjm-2018-0612}, pmid = {31226241}, issn = {1480-3275}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; *Coal Mining ; *Microbiota ; *Wetlands ; }, abstract = {Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%-43%), Bacteroidetes (12%-37%), Firmicutes (3%-11%), and Verrucomicrobia (6%-11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.}, } @article {pmid30769763, year = {2019}, author = {, and Singh, BR and Gupta, VK and Deeba, F and Bajpai, R and Pandey, V and Naqvi, AH and Upreti, DK and Gathergood, N and Jiang, Y and El Enshasy, HA and Sholkamy, EN and Mostafa, AA and Hesham, AE and Singh, BN}, title = {Non-Toxic and Ultra-Small Biosilver Nanoclusters Trigger Apoptotic Cell Death in Fluconazole-Resistant Candida albicans via Ras Signaling.}, journal = {Biomolecules}, volume = {9}, number = {2}, pages = {}, pmid = {30769763}, issn = {2218-273X}, mesh = {Antifungal Agents/chemistry/*pharmacology ; Candida albicans/cytology/*drug effects ; Cell Death ; Cell Survival/drug effects ; Drug Resistance, Fungal/*drug effects ; Fluconazole/chemistry/*pharmacology ; Lichens/chemistry/metabolism ; Metal Nanoparticles/*chemistry ; Particle Size ; Proto-Oncogene Proteins p21(ras)/*antagonists & inhibitors/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; Silver/chemistry/*metabolism ; Surface Properties ; }, abstract = {Silver-based nanostructures are suitable for many biomedical applications, but to be useful therapeutic agents, the high toxicity of these nanomaterials must be eliminated. Here, we biosynthesize nontoxic and ultra-small silver nanoclusters (rsAg@NCs) using metabolites of usnioid lichen (a symbiotic association of algae and fungi) that exhibit excellent antimicrobial activity against fluconazole (FCZ)-resistant Candida albicans that is many times higher than chemically synthesized silver nanoparticles (AgNPs) and FCZ. The rsAg@NCs trigger apoptosis via reactive oxygen species accumulation that leads to the loss of mitochondrial membrane potential, DNA fragmentation, chromosomal condensation, and the activation of metacaspases. The proteomic analysis clearly demonstrates that rsAg@NCs exposure significantly alters protein expression. Most remarkable among the down-regulated proteins are those related to glycolysis, metabolism, free radical scavenging, anti-apoptosis, and mitochondrial function. In contrast, proteins involved in plasma membrane function, oxidative stress, cell death, and apoptosis were upregulated. Eventually, we also established that the apoptosis-inducing potential of rsAg@NCs is due to the activation of Ras signaling, which confirms their application in combating FCZ-resistant C. albicans infections.}, } @article {pmid41239201, year = {2025}, author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A}, title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {86}, pmid = {41239201}, issn = {2730-6844}, support = {SRUG2204254606//National Research Foundation/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration & dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; }, abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.

DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.}, } @article {pmid41239026, year = {2025}, author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H}, title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.}, journal = {Acta parasitologica}, volume = {70}, number = {6}, pages = {211}, pmid = {41239026}, issn = {1896-1851}, support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; }, mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Gastrointestinal Microbiome ; Mice ; *Intestinal Mucosa/pathology/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology/pathology ; Disease Models, Animal ; Feces/microbiology/parasitology ; Female ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.

METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.

RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3 months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6 months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3 months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6 months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6 months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P < 0.01), and reduced goblet cell counts (P < 0.05), collectively indicating compromised intestinal barrier integrity.

CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.}, } @article {pmid41238915, year = {2025}, author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA}, title = {Microbial signals in primary and metastatic brain tumors.}, journal = {Nature medicine}, volume = {31}, number = {11}, pages = {3675-3688}, pmid = {41238915}, issn = {1546-170X}, support = {R21 NS130323/NS/NINDS NIH HHS/United States ; F32 CA260769/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P50 CA221703/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; }, abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.}, } @article {pmid41135729, year = {2025}, author = {Li, M and Wang, H and Chu, H and Wang, Y and Lu, J}, title = {Deciphering microbial dynamics in coastal ecosystems under polycyclic aromatic hydrocarbon stress: Community assembly, interaction networks, and metabolic adaptations.}, journal = {Environmental research}, volume = {287}, number = {}, pages = {123179}, doi = {10.1016/j.envres.2025.123179}, pmid = {41135729}, issn = {1096-0953}, mesh = {*Polycyclic Aromatic Hydrocarbons/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Geologic Sediments/microbiology/chemistry ; Estuaries ; Ecosystem ; Environmental Monitoring ; Rivers/microbiology/chemistry ; China ; }, abstract = {The significant toxicity and carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) have raised increasing concern about their contamination, particularly in coastal regions with intensive human activities and urbanization. However, limited information exists on microbial response mechanisms across varying levels of PAHs contamination. In this study, sediment samples at 18 locations along the Yantai inland river and estuary were collected in October 2024 to examine the partitioning and spatial dispersal of PAHs, while microbial community assembly, interaction networks, and metabolic adaptations were analysed using metagenomics. Results showed that the average ∑PAHs concentration in the estuary (27.95 ± 2.91 ng/g) was significantly lower than that in the river (77.54 ± 43.39 ng/g), with a correspondingly higher ecological risk in the river. High-molecular-weight (HMW) PAHs dominated in both estuary and river sediments due to their high hydrophobicity and stability. Microbial community analysis revealed increased microbial diversity and a higher abundance of PAHs-degrading microbes (e.g., Ruegeria, known for degrading low-molecular-weight PAHs) under higher PAHs contamination. Co-occurrence network and topological analyses demonstrated dual regulatory effects of PAHs stress on microbial interactions, where elevated PAHs contamination intensified interspecies connectivity while simultaneously inducing destabilizing negative covariance patterns that weakened microbial network integrity. Additionally, neutral community model analysis indicated that stochastic processes dominated community assembly, with higher proportions of stochasticity observed in rivers under high PAHs stress. Notably, elevated PAHs concentrations significantly impaired energy metabolism and nitrogen metabolic pathways (p < 0.05), suggesting altered nitrogen biogeochemistry under PAHs contamination. This study advances the understanding of microbial population responses to different PAHs contamination levels in coastal regions.}, } @article {pmid40694261, year = {2025}, author = {Tay, DD and Kumar, VS and Shapawi, R and Shah, MD and Ahmad, HF and Mazlan, N}, title = {The Relationship Between the Gut Microbiome and the Aqua Cultured Fish, General Prospects Toward Fish Health: A Systematic Review.}, journal = {Applied biochemistry and biotechnology}, volume = {197}, number = {10}, pages = {6314-6357}, pmid = {40694261}, issn = {1559-0291}, support = {Grant Agensi Kerajaan HIC2404//Ministry of Higher Education, Malaysia/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Fishes/microbiology ; *Aquaculture ; }, abstract = {Aquaculture allows the cultivation of aquatic life outside its normal origins which can provide work opportunities, seafood security, as well as conservation efforts for endangered fish species. Numerous factors influence the health of aquaculture fish, with the gut microbiome playing a pivotal role. Research indicates that an imbalance or dysbiosis in the gut microbiome can significantly affect the overall well-being and health outcome of these fish. Despite extensive research utilizing metagenomics across diverse environments and controlled conditions, a clear consensus on the characteristic of "healthy" or "optimal" gut microbiome in domesticated fish has yet to be established. This review will cover 28 studies, which further discusses the findings of the gut microbiome within fish and attempts to provide a general outline of how the gut bacteria may interact and affect fish health within aquaculture environments. The indices as well as pathogens and beneficial bacteria of each study are also listed. This review aims to provide readers with an enhanced understanding of the complex dynamics of the gut microbiome in aquaculture fish, while offering insights that could inform the design of future studies in this field.}, } @article {pmid41238729, year = {2025}, author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY}, title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39988}, pmid = {41238729}, issn = {2045-2322}, support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, the Ministry of Food and Drug Safety)/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; }, abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.}, } @article {pmid41236788, year = {2025}, author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C}, title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e72950}, doi = {10.2196/72950}, pmid = {41236788}, issn = {1929-0748}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists & inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; }, abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.

OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.

METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.

RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.

CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.

TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.

DERR1-10.2196/72950.}, } @article {pmid41236031, year = {2025}, author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ}, title = {Altered oral microbiome diversity in patients with oral candidiasis.}, journal = {Archives of oral biology}, volume = {180}, number = {}, pages = {106430}, doi = {10.1016/j.archoralbio.2025.106430}, pmid = {41236031}, issn = {1879-1506}, mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; }, abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.

DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.

RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.

CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.}, } @article {pmid41235136, year = {2025}, author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y}, title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {9993-10010}, pmid = {41235136}, issn = {1177-8881}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; }, abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.

METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.

RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.

CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.}, } @article {pmid41233937, year = {2025}, author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M}, title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {231}, pmid = {41233937}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.

RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.

CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.}, } @article {pmid41233936, year = {2025}, author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS}, title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {234}, pmid = {41233936}, issn = {2049-2618}, support = {141954/2019-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; }, abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.

RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.

CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.}, } @article {pmid41233919, year = {2025}, author = {Vohsen, SA and Gruber-Vodicka, HR and Osman, EO and Saxton, MA and Joye, SB and Dubilier, N and Fisher, CR and Baums, IB}, title = {Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {232}, pmid = {41233919}, issn = {2049-2618}, support = {ECOGIG//Gulf of Mexico Research Initiative/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; *Sulfur/metabolism ; Symbiosis ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Chemoautotrophic Growth ; Metagenomics/methods ; Seawater/microbiology ; }, abstract = {BACKGROUND: Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with related bacteria and report here that these associations are widespread.

RESULTS: We screened corals, water, and sediment for Thioglobaceae using 16S metabarcoding and found ASVs associated with corals at high relative abundance (10 - 91%). These ASVs were specific to coral hosts, absent in water samples, and rare or absent in sediment samples. Using metagenomics and transcriptomics, we assembled the genome of one phylotype associated with Paramuricea sp. B3 (ASV 4) which contained the genetic potential to oxidize sulfur and fix carbon, and confirmed that these pathways were transcriptionally active. Furthermore, its relative abundance was negatively correlated with the stable isotopic composition of its host coral's tissue suggesting some contribution of chemoautotrophy to the coral holobiont.

CONCLUSIONS: We propose that some lineages of Thioglobaceae may facultatively supplement the diet of their host corals through chemoautotrophy at seeps or may provide essential amino acids or vitamins. This is the first documented association between chemoautotrophic symbionts and corals at seeps and suggests that the footprint of chemosynthetic environments is wider than currently understood.}, } @article {pmid41233799, year = {2025}, author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA}, title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1276}, pmid = {41233799}, issn = {1479-5876}, mesh = {*Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Skin/microbiology ; Metagenomics ; *Dermatology/methods ; }, abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.

METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.

RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.

CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.}, } @article {pmid41137451, year = {2025}, author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J}, title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.}, journal = {Molecular ecology}, volume = {34}, number = {22}, pages = {e70156}, doi = {10.1111/mec.70156}, pmid = {41137451}, issn = {1365-294X}, support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; }, mesh = {*Methane/biosynthesis ; *Soil Microbiology ; *Soil/chemistry ; Temperature ; *Food Chain ; Microbiota/genetics ; Oryza ; Metagenomics ; Anaerobiosis ; Climate Change ; }, abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.}, } @article {pmid41124778, year = {2025}, author = {Ohlsson, C and Li, L and Horkeby, K and Lawenius, L and Colldén, H and Sjögren, K and Baldanzi, G and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Grahnemo, L}, title = {The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5α-reductase activity in females.}, journal = {EBioMedicine}, volume = {121}, number = {}, pages = {105978}, pmid = {41124778}, issn = {2352-3964}, mesh = {Humans ; Female ; *Dihydrotestosterone/blood ; Male ; Middle Aged ; *Testosterone/blood ; *Gastrointestinal Microbiome ; Aged ; *3-Oxo-5-alpha-Steroid 4-Dehydrogenase/metabolism/genetics ; Cross-Sectional Studies ; Animals ; }, abstract = {BACKGROUND: Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5α-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5α-reductase activity or altered β-glucuronidase-induced androgen reabsorption from the gut.

METHODS: We used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.

FINDINGS: We confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5α-reductase type 1 (P = 3 × 10[-4]), but not β-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5α-reductase type 1 (P < 2 × 10[-149]) and the circulating DHT/T ratio (O. splanchnicus P = 3 × 10[-6]; P. distasonis P = 5 × 10[-5]). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).

INTERPRETATION: These findings demonstrate that the circulating DHT/T ratio is increased by GM 5α-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.

FUNDING: See Acknowledgements.}, } @article {pmid40967080, year = {2025}, author = {Chen, J and Li, W and Yang, L and Li, J and Wang, S and Chen, Z and Xu, S and Wen, M and Liang, J and Hu, Z and Pan, F and He, L and Gu, L and Wang, Z and Chen, H and Guo, Z}, title = {Microbiota-derived butyrate potentiates MSLN CAR-T cell therapy by metabolic reprogramming and extracellular matrix remodeling.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {192}, number = {}, pages = {118560}, doi = {10.1016/j.biopha.2025.118560}, pmid = {40967080}, issn = {1950-6007}, mesh = {Humans ; *Immunotherapy, Adoptive/methods ; *Extracellular Matrix/metabolism/drug effects ; *Butyric Acid/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Receptors, Chimeric Antigen/metabolism/immunology ; Cell Line, Tumor ; *T-Lymphocytes/immunology/drug effects/metabolism ; Male ; *Butyrates ; Female ; Metabolic Reprogramming ; }, abstract = {Despite the success of chimeric antigen receptor (CAR)-T cell therapy in hematologic malignancies, its efficacy in solid tumors remains limited due to T cell dysfunction and immunosuppressive microenvironments. Emerging evidence suggests that gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), may enhance T cell function, but their role in CAR-T therapy is unexplored. Here, in a small patient cohort (n = 4), preliminary metagenomic and metabolomics data suggested an association between higher butyrate levels and improved CAR-T responses, motivating our investigation of sodium butyrate (NaB), a microbiota-derived short-chain fatty acid, as a potential enhancer of CAR-T cell function through integrated metabolic and transcriptional reprogramming. Functional screening showed that NaB treatment augmented CAR-T cell antitumor activity while promoting a memory-like phenotype and reducing exhaustion markers. Mechanistically, NaB amplified antigen-driven phosphorylation of signaling effectors (p-ERK1/2, p-ZAP-70, p-AKT), inducing dual activation of glycolytic and oxidative phosphorylation pathways, coupled with upregulation of extracellular matrix (ECM)-remodeling genes (MMPs, Collagens), thereby improving tumor homing capacity. These preliminary findings suggest NaB as a potential link between microbial metabolism and CAR-T cell efficacy, offering a promising yet exploratory strategy to optimize adoptive immunotherapy through signaling-metabolic-ECM crosstalk, pending validation in larger cohorts.}, } @article {pmid40930091, year = {2025}, author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP}, title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.}, journal = {Cell}, volume = {188}, number = {23}, pages = {6666-6686.e25}, doi = {10.1016/j.cell.2025.08.020}, pmid = {40930091}, issn = {1097-4172}, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Genome-Wide Association Study ; Child, Preschool ; Child ; Male ; Infant ; Female ; *Malnutrition/microbiology/genetics ; Malawi ; Longitudinal Studies ; }, abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.}, } @article {pmid40902595, year = {2025}, author = {Guinet, B and Oskolkov, N and Moreland, K and Dehasque, M and Chacón-Duque, JC and Angerbjörn, A and Arsuaga, JL and Danilov, G and Kanellidou, F and Kitchener, AC and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Termes, L and Zazula, G and Mortensen, P and Grigorieva, L and Richards, M and Shapiro, B and Lister, AM and Vartanyan, S and Díez-Del-Molino, D and Götherström, A and Pečnerová, P and Nikolskiy, P and Dalén, L and van der Valk, T}, title = {Ancient host-associated microbes obtained from mammoth remains.}, journal = {Cell}, volume = {188}, number = {23}, pages = {6606-6619.e24}, doi = {10.1016/j.cell.2025.08.003}, pmid = {40902595}, issn = {1097-4172}, mesh = {Animals ; *Mammoths/microbiology ; Phylogeny ; *DNA, Ancient/analysis ; *Microbiota/genetics ; *Fossils/microbiology ; Elephants/microbiology ; Erysipelothrix/genetics/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.}, } @article {pmid40865528, year = {2025}, author = {Shi, Y and Li, Y and Li, H and Haerheng, A and Marcelino, VR and Lu, M and Lemey, P and Tang, J and Bi, Y and Pettersson, JH and Bohlin, J and Klaps, J and Wu, Z and Wan, W and Sun, B and Kang, M and Holmes, EC and He, N and Su, S}, title = {Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.}, journal = {Cell}, volume = {188}, number = {23}, pages = {6591-6605.e14}, doi = {10.1016/j.cell.2025.08.016}, pmid = {40865528}, issn = {1097-4172}, mesh = {Animals ; *Mammals/microbiology/virology ; Humans ; *Public Health Surveillance ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Microbiota/genetics ; Animals, Wild/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Animals, Domestic/microbiology/virology ; Viruses/genetics/isolation & purification ; Phylogeny ; }, abstract = {Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.}, } @article {pmid39621289, year = {2025}, author = {Salam, LB and Apollos, EE and Obayori, OS and Michael, GI}, title = {Physicochemistry and comparative metagenomics of a tropical estuary persistently inundated with anthropogenic pollutants.}, journal = {Folia microbiologica}, volume = {70}, number = {5}, pages = {979-1013}, pmid = {39621289}, issn = {1874-9356}, mesh = {*Estuaries ; Metagenomics ; *Geologic Sediments/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Polycyclic Aromatic Hydrocarbons/analysis ; Microbiota ; Metagenome ; *Seawater/chemistry/microbiology ; Tropical Climate ; }, abstract = {The physicochemistry, metabolic properties, and microbial community structure of a tropical estuary persistently inundated with anthropogenic pollutants were elucidated using diverse analytical tools and a shotgun metagenomics approach. The physicochemistry of the Awoye estuary surface water (AEW) and sediment (AES) revealed higher values in the sediment for most of the parameters analyzed, while aside from copper and zinc, the concentrations of the detected heavy metals (Cd, Cr, Pb, Fe, As, Ni, Hg, Mn, Se) in the water and sediment were higher than the acceptable thresholds. Hydrocarbon content analysis revealed increasingly high concentrations of high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) in the sediment. Structurally, the predominant taxa in the AEW metagenome are Proteobacteria (50.35%), Alphaproteobacteria (43.31%), Brevundimonas (49.96%), and Leptolyngbya boryana (14.93%), while in the sediment (AES) metagenome, Proteobacteria (53.03%), Gammaproteobacteria (28.66%), Azospirillum (6.51%), and Acidihalobacter prosperus (7.56%) were preponderant. Statistical analysis of the two microbiomes (AEW, AES) revealed significant statistical differences (P < 0.05) at all the hierarchical levels. Functional characterization of the two metagenomes revealed extensive adaptations of the sediment microbiome to various environmental stressors as evident in the high numbers of putative genes involved in the degradation of diverse classes of aromatic hydrocarbons, efflux, detoxification, and transport of heavy metals, and metabolism of organic/inorganic nutrients. Findings from this study revealed that the estuary sediment is the sink for most of the anthropogenic pollutants and harbors the more adapted microbiome that could serve as a potential bioresource for the bioremediation of the perturbed estuary.}, } @article {pmid41233350, year = {2025}, author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW}, title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1782}, pmid = {41233350}, issn = {2052-4463}, support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; }, mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; }, abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.}, } @article {pmid41233306, year = {2025}, author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X}, title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9980}, pmid = {41233306}, issn = {2041-1723}, support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; }, abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.}, } @article {pmid41231980, year = {2025}, author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH}, title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.}, journal = {Science (New York, N.Y.)}, volume = {390}, number = {6774}, pages = {eadx7604}, doi = {10.1126/science.adx7604}, pmid = {41231980}, issn = {1095-9203}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth & development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.}, } @article {pmid41231285, year = {2025}, author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN}, title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {191}, pmid = {41231285}, issn = {1572-9699}, support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; }, mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; }, abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.}, } @article {pmid41231233, year = {2025}, author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE}, title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.}, journal = {Microbial genomics}, volume = {11}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001510}, pmid = {41231233}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; }, abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.}, } @article {pmid41229166, year = {2025}, author = {Houttu, N and Mokkala, K and Lindgren, H and Lotankar, M and Benchraka, C and Pärnänen, K and Saros, L and Muhli, E and Vahlberg, T and Lahti, L and Laitinen, K}, title = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70128}, doi = {10.1002/mbo3.70128}, pmid = {41229166}, issn = {2045-8827}, support = {//This clinical trial was supported by the State Research Funding for university-level health research in the Turku University Hospital Expert Responsibility Area, Research Council of Finland (#258606), the Diabetes Research Foundation, the Juho Vainio Foundation, the Finnish Cultural Foundation, Päivikki and Sakari Sohlberg Foundation, Sigrid Juselius Foundation, and the Finnish Foundation for Cardiovascular Research. Funding to the University of Turku for the metagenomics analyses was provided by Janssen Research and Development, LLC. Himmi Lindgren was partially supported by the Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC)./ ; }, mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Adiposity ; *Postpartum Period ; Adult ; Body Mass Index ; *Obesity/microbiology ; Metagenomics ; Young Adult ; Bacteria/classification/genetics/isolation & purification ; Overweight/microbiology ; Waist-Hip Ratio ; }, abstract = {Gut microbiota is linked with health, including obesity, in the general population. It is unknown whether adiposity at postpartum is influenced by gut microbiota already during pregnancy. We investigated the association between the gut microbiota's composition and predicted function by metagenomics during pregnancy and the women's adiposity (body mass index [BMI], waist-to-hip ratio [WHR], body fat%) assessed at 1-, 2-, and 5-6-years' postpartum in 257 women with overweight or obesity based on prepregnancy BMI values. Body fat% at 1-year, but not at 2- or 5-6-years' postpartum, was associated inversely with α-diversity during pregnancy. Bacterial species GGB3034 SGB4030 (family Erysipelotrichaceae) was higher in women with normal weight than those in women with obesity at 1-year postpartum (q = 0.02), other species being borderline statistically significant (q < 0.25). High WHR and body fat% at 1-year postpartum were associated with two species (q < 0.25). Considering predicted functions of bacteria, an association was detected for BMI, WHR, and body fat%, e.g., body fat% and glycogen biosynthesis I (q < 0.25). Gut microbiota during pregnancy predicted the BMI and body fat% at 1-year postpartum (ROC > 0.50, p < 0.02). Postpartum adiposity was associated with several species and α-diversity. Gut microbiota during pregnancy may be involved in the persistence of obesity and its comorbidities after pregnancy.}, } @article {pmid41228422, year = {2025}, author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S}, title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, doi = {10.3390/nu17213350}, pmid = {41228422}, issn = {2072-6643}, support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; }, abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.}, } @article {pmid41228409, year = {2025}, author = {Xu, C and Cui, H and Fang, Q and Tu, P and Cui, X}, title = {Steamed Panax notoginseng Saponins Ameliorate Cyclophosphamide-Induced Anemia by Attenuating Gut-Liver Injury and Activating the cAMP/PI3K/AKT Signaling Pathway.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, doi = {10.3390/nu17213335}, pmid = {41228409}, issn = {2072-6643}, support = {202202AG050021//the Yunnan Major Scientific and Technological Projects/ ; }, mesh = {Animals ; *Saponins/pharmacology ; *Panax notoginseng/chemistry ; *Cyclophosphamide/adverse effects ; Signal Transduction/drug effects ; *Anemia/chemically induced/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Cyclic AMP/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism ; Colon/metabolism/drug effects ; }, abstract = {Background: Steamed Panax notoginseng saponins (SPNSs) can alleviate cyclophosphamide-induced anemia. However, the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia remain unexplored. Objective: To elucidate the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia. Methods: Blood samples were collected and analyzed on days 7 and 14. Liver tissues and small intestinal villi structures were observed via HE staining. Liver and colon content metabolites were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Liver proteins were analyzed by using an Orbitrap Astral mass spectrometer. Colon content microbiota composition was assessed via metagenomics. Signaling pathway protein expression was analyzed via Western blotting (WB). Results: SPNSs significantly increased the red blood cell (RBC) count and hemoglobin (HGB) level by day 14 and alleviated hepatointestinal damage. Hepatic metabolomics revealed: the most abundant metabolites were fatty acids and stachyose on day 7 and amino acid and arachidonic acid derivatives on day 14. KEGG analysis implicated cAMP signaling. Proteomics revealed upregulated immune-related proteins and enhanced PI3K pathway activity (WB-validated). Colon content metabolomics showed increased daidzein, 3-(2,5-dimethoxyphenyl) propanoic acid, γ-CEHC, and adenosine in SPNS groups on day 14. Metagenomics indicated differential abundances of Heminiphilus faecis, Phocaeicola sartorii, and s-bacterium_J10.2018 on day 14. Multiomics integration demonstrated significant correlations between hepatic metabolites, hematopoietic proteins, colon content metabolites, and probiotic bacteria. Conclusions: SPNS alleviates cyclophosphamide-induced hepato-intestinal injury in anemic mice by modulating the gut microbiota and enhancing hepato-intestinal immune defense. Additionally, SPNSs ameliorate anemia in cyclophosphamide-treated mice by activating the cAMP/PI3K/AKT pathway, promoting hepatocyte proliferation, and increasing hematopoietic protein expression.}, } @article {pmid41226831, year = {2025}, author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E}, title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, doi = {10.3390/ijms262110796}, pmid = {41226831}, issn = {1422-0067}, support = {КП-06-Н83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; }, mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; }, abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.}, } @article {pmid41226812, year = {2025}, author = {Kondo, T and Kondo, S and Nakayama-Imaohji, H and Tada, A and Tabassum, N and Munyeshyaka, E and Koyano, K and Nakamura, S and Kusaka, T and Kuwahara, T}, title = {Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, doi = {10.3390/ijms262110775}, pmid = {41226812}, issn = {1422-0067}, support = {24K14726//JSPS KAKENHI/ ; 23K28020//JSPS KAKENHI/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; *Intestinal Mucosa/microbiology/pathology ; Adolescent ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Dysbiosis/microbiology ; }, abstract = {Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease, are chronic disorders relating to gut microbiota dysbiosis. Despite severe pancolitis being more prevalent in pediatric UC than in adults, alterations in the colon mucosa-associated microbiota (MAM) and their association with disease severity remain to be elucidated. The present study aimed to compare the gut microbiota in colon lavage fluids (CLFs) and fecal samples from 19 pediatric UC and 19 non-IBD patients. The community structure of MAM inferred by 16S metagenomic analysis was similar throughout the colon regardless of disease type. Bacterial compositions between MAM and feces were significantly different in non-IBD, while no difference was observed in pediatric UC, indicating a compromised mucous layer that could not sufficiently separate the MAM and luminal microbiota in UC. In pediatric UC, homogenous distribution of MAM was gradually disordered with increases in disease activity or mucosal inflammation, and bacterial groups of upper digestive tract or environmental origin were more abundant in MAM. Monitoring key bacterial markers in MAM, which include Lactobacillus and Enterococcus or Faecalibacterium and Blautia as increased or reduced members in pediatric UC, respectively, might be useful for evaluation of patient prognosis.}, } @article {pmid41226502, year = {2025}, author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT}, title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, doi = {10.3390/ijms262110463}, pmid = {41226502}, issn = {1422-0067}, support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; }, abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.}, } @article {pmid41225454, year = {2025}, author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T}, title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.}, journal = {BMC pregnancy and childbirth}, volume = {25}, number = {1}, pages = {1198}, pmid = {41225454}, issn = {1471-2393}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; }, abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).

METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n = 31) and those with normal thyroid function (Control group, n = 30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16 S rRNA metagenomic sequencing.

RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p = 0.034; Shannon index, p = 0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p = 0.002, p = 0.049, and p = 0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.

CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.}, } @article {pmid41225248, year = {2025}, author = {Bignami, G and Monzón-Atienza, L and Leuzzi, D and Scicchitano, D and Candela, M and Gómez-Mercader, A and Jlidi, M and Gustinelli, A and Tedesco, P and Fioravanti, ML and Castro, PL and Acosta, F}, title = {"Effects of Bacillus Velezensis D-18 on Health Status of European Seabass (Dicentrarchus labrax) Experimentally Challenged with Vibrio harveyi".}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41225248}, issn = {1867-1314}, support = {28740//Horizon 2020/ ; }, abstract = {In recent years, the use of probiotics as a possible alternative to antibiotics has generated a growing interest in the global aquaculture field. In this study, the probiotic Bacillus velezensis D-18 was evaluated for its potential protective effect against the marine pathogen Vibrio harveyi. The probiotic was administered through the diet of European seabass (Dicentrarchus labrax) for 30 days, followed by an in vivo challenge with V. harveyi to assess whether the D-18 strain could enhance host resistance to infection. Biofilm formation in tanks was also investigated to analyze its composition and if there are antagonistic interactions between the two bacterial species. From a histological perspective, significant changes were observed in intestinal morphological parameters after infection, the area and base of the villi appeared to increase in the probiotic-fed groups as did the number of goblet cells and in the serum antibacterial activity which was increased in the infected group that received the probiotic compared to baseline levels. The intestinal microbiome was also analyzed to monitor the composition and determine whether different diets before and after infection induced any changes. Although no significant differences were found in the metagenomics of the tank biofilm and the gut microbiome, mortality rates showed that the probiotic provided effective protection against the pathogen. These findings support the potential of B. velezensis D-18 as a viable alternative to antibiotics, particularly when included in the diet prior to disease onset.}, } @article {pmid41225104, year = {2026}, author = {Kars, G and Alkebsi, BLA and Keleş, S and Altan, H and Özer, H and Holyavkin, C and Karaselek, MA}, title = {Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.}, journal = {Advances in experimental medicine and biology}, volume = {1492}, number = {}, pages = {291-313}, pmid = {41225104}, issn = {0065-2598}, mesh = {Humans ; *Dental Caries/microbiology/immunology ; *Microbiota/immunology ; Child ; Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; }, abstract = {Inborn errors of immunity (IEIs) are genetic disorders that impair immune defense and regulation, increasing susceptibility to infections, including those in the oral cavity. The oral microbiota plays a vital role in maintaining oral health, and in pediatric patients with IEIs, disruptions in this balance can lead to dental caries and other oral diseases. This chapter provides a comprehensive analysis of the relationship between immune deficiencies and oral microbiota dysbiosis, focusing on dental caries in children with IEIs. Omics technologies, particularly metagenomics, have enhanced understanding of the microbial diversity and metabolic activities within the oral microbiota of the patients. Key findings reveal that compromised immune responses in children with IEIs disrupt the balance of oral bacteria, making them more prone to dental caries. The chapter highlights the importance of an interdisciplinary approach, integrating microbiology, immunology, dentistry, and bioinformatics, to uncover the complex interactions between the oral microbiome and the immune system. The insights gained from this research will contribute to the development of personalized therapeutic strategies, improving the dental and overall health of pediatric patients with IEIs.}, } @article {pmid41225090, year = {2026}, author = {Ziaei, H and Rezaei, N}, title = {Introduction to Oral Immunity.}, journal = {Advances in experimental medicine and biology}, volume = {1492}, number = {}, pages = {3-21}, pmid = {41225090}, issn = {0065-2598}, mesh = {Humans ; *Mouth/immunology/microbiology ; Microbiota/immunology ; Animals ; *Immunity, Innate ; *Immunity, Mucosal ; *Mouth Mucosa/immunology/microbiology ; Adaptive Immunity ; }, abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.}, } @article {pmid41224755, year = {2025}, author = {Gupta, S and Almeida, A}, title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9959}, pmid = {41224755}, issn = {2041-1723}, support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/isolation & purification/classification/pathogenicity ; Humans ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Klebsiella Infections/microbiology ; *Metagenome/genetics ; Metagenomics/methods ; Virulence Factors/genetics ; Genetic Variation ; }, abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.}, } @article {pmid41218045, year = {2025}, author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N}, title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336700}, pmid = {41218045}, issn = {1932-6203}, mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Photobacterium/genetics/isolation & purification ; Phylogeny ; Thailand ; Vibrio/genetics/isolation & purification ; }, abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.}, } @article {pmid41212311, year = {2025}, author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY}, title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {3}, pages = {42}, pmid = {41212311}, issn = {1433-4909}, mesh = {*Hot Springs/microbiology ; *Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; Russia ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.}, } @article {pmid41187758, year = {2025}, author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and , and König, B and Sauer, U and Stelling, J and Macpherson, AJ}, title = {A global survey of taxa-metabolic associations across mouse microbiome communities.}, journal = {Cell host & microbe}, volume = {33}, number = {11}, pages = {1960-1976.e10}, doi = {10.1016/j.chom.2025.10.010}, pmid = {41187758}, issn = {1934-6069}, mesh = {Animals ; Mice/microbiology ; *Microbiota/physiology ; Metabolomics ; *Bacteria/classification/metabolism/genetics ; Host Microbial Interactions ; Symbiosis ; }, abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.}, } @article {pmid41183305, year = {2025}, author = {Yang, R and Ma, J and Abebe, H and Tu, Y}, title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {45}, pages = {28711-28723}, doi = {10.1021/acs.jafc.5c08498}, pmid = {41183305}, issn = {1520-5118}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Salinity ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Sodium Chloride/analysis/metabolism ; Sodium/analysis/metabolism ; }, abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.}, } @article {pmid41167188, year = {2025}, author = {Cha, JH and Kim, N and Ma, J and Lee, S and Koh, G and Yang, S and Beck, S and Byeon, I and Lee, B and Lee, I}, title = {A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights.}, journal = {Cell host & microbe}, volume = {33}, number = {11}, pages = {1977-1994.e8}, doi = {10.1016/j.chom.2025.10.001}, pmid = {41167188}, issn = {1934-6069}, mesh = {Humans ; *Mouth/microbiology ; *Phylogeny ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Periodontitis/microbiology ; Metagenome ; Genomics ; Gastrointestinal Microbiome/genetics ; }, abstract = {The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 previously unidentified species, improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 previously uncharacterized candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota and distinct from environmental Patescibacteria. Additionally, an oral CPR subclade is associated with periodontitis, complementing Porphyromonas gingivalis in predicting disease. Finally, comparing HROM with reference genomes of the gut microbiome reveals taxonomic and functional divergence between these microbiomes. HROM contains 42 ectopic oral species, and their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases. Thus, HROM offers an expanded view of the oral microbiome and highlights the clinical importance of further examining the links between oral microbes and systemic disorders.}, } @article {pmid41128819, year = {2025}, author = {Zhao, Y and Chen, J and Zhu, S and Xu, Y and Zhu, J and Yang, J and Zhou, W and Yang, Y and Lin, M and Chen, Q and Xia, M and Chen, Y and Liu, Y}, title = {Olsenella scatoligenes-derived skatole promotes smooth muscle cell proliferation and migration to aggravate atherosclerosis.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf238}, pmid = {41128819}, issn = {1751-7370}, support = {2025QNPY01//Fundamental Research Funds for the Central Universities/ ; 2024A04J6477//Guangzhou Science and Technology Project/ ; 82273611//National Natural Science Foundation of China/ ; 21HAA01094//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 82330105//Key Program of National Natural Science Foundation of China/ ; }, mesh = {*Cell Proliferation ; Humans ; *Cell Movement ; *Atherosclerosis/microbiology/pathology ; *Myocytes, Smooth Muscle/physiology ; Male ; Animals ; Calcium-Binding Proteins/metabolism/genetics ; Microfilament Proteins/metabolism/genetics ; Calponins ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/genetics ; Female ; Muscle, Smooth, Vascular ; *Actinobacteria/metabolism ; Mice ; Middle Aged ; Coronary Artery Disease/microbiology ; }, abstract = {Coronary artery disease (CAD) remains the leading cause of mortality and morbidity globally. The gut microbiota has been implicated in the development of CAD through unclear mechanisms. Here, we demonstrate that the abundance and interspecies interactions of Olsenella scatoligenes are 4.7- and 1.6-fold higher in patients with CAD, respectively, and positively associated with disease severity. Furthermore, integrative metagenomic and metabolomic analyses identify skatole as the key microbial effector mediating the pro-atherogenic effect of O. scatoligenes. Consistently, supplementation with O. scatoligenes or skatole results in 1.26- and 1.23-fold increases in aortic plaque area, respectively, by promoting vascular smooth muscle cell proliferation and migration to the intima. Mechanistically, O. scatoligenes-derived skatole facilitates nuclear translocation of the aryl hydrocarbon receptor and enhances its binding to the promoter region of calponin 1. Silencing either aryl hydrocarbon receptor or calponin 1 attenuates ~40% of the vascular smooth muscle cell proliferation and migration induced by skatole. Collectively, our study identifies increased skatole production as the principal microbial effector linking O. scatoligenes to aggravated atherosclerosis through activation of the aryl hydrocarbon receptor-calponin 1 axis and underscores the therapeutic potential of targeting skatole production for the management of CAD.}, } @article {pmid41118772, year = {2025}, author = {Jacoby, C and Scorza, K and Ecker, L and Nol Bernardino, P and Little, AS and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH}, title = {Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.}, journal = {Cell host & microbe}, volume = {33}, number = {11}, pages = {1873-1885.e7}, doi = {10.1016/j.chom.2025.09.014}, pmid = {41118772}, issn = {1934-6069}, mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; *Steroids/metabolism ; *Clostridium/metabolism/genetics/enzymology/isolation & purification ; Crohn Disease/microbiology/drug therapy ; Germ-Free Life ; Hydrocortisone/metabolism ; Prednisolone/metabolism ; Metabolic Networks and Pathways ; *Oxidoreductases/metabolism/genetics ; *Gastrointestinal Tract/microbiology ; Glucocorticoids/metabolism ; Oxidation-Reduction ; }, abstract = {Steroid hormone metabolism by the gut microbiome affects host physiology, however, the underlying microbial pathways remain incompletely understood. Here, we isolate a gut bacterial species, which we designate Clostridium steroidoreducens, that reduces cortisol and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-a frontline Crohn's disease therapy. OsrB is a 3-oxo-Δ[4]-steroid reductase that converts steroid hormones to 5β-dihydrosteroid intermediates, which OsrC subsequently reduces to 3β,5β-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in metagenomes of Crohn's disease patients. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.}, } @article {pmid41106786, year = {2025}, author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z}, title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.}, journal = {Fitoterapia}, volume = {187}, number = {}, pages = {106935}, doi = {10.1016/j.fitote.2025.106935}, pmid = {41106786}, issn = {1873-6971}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology ; *Acute Lung Injury/drug therapy/etiology/microbiology ; *Sepsis/complications ; Male ; Mice, Inbred C57BL ; Drug Combinations ; Panax/chemistry ; Ophiopogon/chemistry ; Cytokines ; *Steroids/biosynthesis ; }, abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.}, } @article {pmid41067450, year = {2026}, author = {Liu, N and Zhang, Y and Zhang, Y and Yang, Y and Long, H and Huang, A and Zeng, Y and Xie, Z}, title = {Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems.}, journal = {Bioresource technology}, volume = {440}, number = {}, pages = {133459}, doi = {10.1016/j.biortech.2025.133459}, pmid = {41067450}, issn = {1873-2976}, mesh = {*Quorum Sensing/physiology ; *Aquaculture/methods ; Animals ; *Penaeidae/microbiology/metabolism ; *Nitrogen/metabolism ; *Microbiota/physiology ; Nitrites/metabolism ; Ammonia/metabolism ; }, abstract = {Biofloc technology (BFT) enables sustainable aquaculture by leveraging microbial communities to enhance water quality and nutrient cycling. However, the role of quorum sensing (QS) in regulating microbial dynamics and metabolic functions within BFT systems remains poorly understood. This study examined how QS spatiotemporally regulates microbial succession and nutrient metabolism in a biofloc-based Litopenaeus vannamei aquaculture system over 82 days culture. Ammonia and nitrite concentrations shifted through four phases: initial (IP), rising (RP), declining (DP), and stabilization (SP). Notably, nitrite levels decreased rapidly from 1.21 mg/L to 0.03 mg/L during DP. Metagenomic analysis revealed Pseudomonadota, Actinomycetota, and Bacteroidota as the consistently dominant phyla, while dominant genera shifted over time. QS pathways displayed temporal heterogeneity: acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) predominated during IP, whereas aromatic hydrocarbon kinases (AHKs) and cyclic dimeric guanosine monophosphate (c-di-GMP) were more enriched during SP. KEGG analysis indicated that nitrogen metabolism genes were more abundant in bioflocs than in the water. Genes associated with dissimilatory nitrate reduction and denitrification were significantly more abundant than those involved in other nitrogen metabolic processes (p < 0.05). Furthermore, QS signaling coordinated the complex interaction networks among 30 dominant bacterial genera (e.g., Amaricoccus and Ruegeria) involved in carbon, nitrogen, and sulfur metabolism, which is crucial for maintaining the stability and functionality of the biofloc system. This study elucidates the mechanisms through which microbial signaling orchestrates efficient nitrogen removal and sustains system stability, thereby providing a foundation for developing targeted bioaugmentation strategies to enhance sustainable aquaculture practices.}, } @article {pmid41055380, year = {2025}, author = {Du, J-Y and Zhang, Z-J and Tan, L and Yang, J-Y and Yang, R-N and Chen, Y-L and Tan, G-F and Li, J and Li, W-J and Yang, L and Cai, J and Shen, D-L and Zhu, H-R and Fan, Z-X and Yuan, M-L and Zhang, W}, title = {Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.}, journal = {mBio}, volume = {16}, number = {11}, pages = {e0244725}, pmid = {41055380}, issn = {2150-7511}, support = {ZYJC21004//1.3.5 project for disciplines of excellence/ ; 82401769//National Natural Science Foundation of China/ ; 2025ZNSFSC//Department of Science and Technology of Sichuan Province/ ; 2023NSFSC1935//Sichuan science and technology program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/microbiology/complications/metabolism/epidemiology ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Depressive Disorder, Major/microbiology/complications/metabolism/epidemiology ; *Bile Acids and Salts/metabolism ; Middle Aged ; Feces/microbiology ; Metagenomics ; Comorbidity ; Metabolomics ; }, abstract = {Major depressive disorder (MDD) and irritable bowel syndrome (IBS) exhibit high comorbidity, yet their shared pathophysiology remains unclear. Previous studies have primarily focused on the psychological health in the IBS population, without considering psychiatric diagnoses or stratifying different psychological states, potentially leading to biased findings. This study employed multi-omics approaches to characterize gut microbiota and serum metabolites in 120 MDD patients (47 with IBS and 73 without IBS) and 70 healthy controls (HCs). MDD with IBS patients showed significantly higher depression (Hamilton depression scale [HAMD-17]) and anxiety (Hamilton anxiety scale [HAMA-14]) scores than MDD-only patients (P < 0.05). Metagenomic sequencing of fecal samples revealed increased alpha diversity (Chao1/Shannon indices) and Firmicutes dominance in both MDD groups vs HC, while Actinobacteria enrichment specifically marked MDD with IBS. Functionally, MDD with IBS uniquely activated D-amino acid/glycerolipid metabolism pathways (Kyoto Encyclopedia of Genes and Genomes). Serum metabolomics identified comorbid-specific perturbations: downregulation of bile acids (CDCA, GCDCA, GCDCA-3S) and upregulation of glyceric acid/glutaconic acid. Our study also found that Eggerthella lenta and Clostridium scindens are differentially abundant bacteria that are involved in bile acid metabolism, and that microbial genes (e.g., K03738) are associated with glyceric acid production. These findings implicate gut microbiota-driven bile acid/glyceric acid dysregulation in MDD with IBS comorbidity, supporting the gut-brain axis as a therapeutic target for probiotics or microbiota transplantation.IMPORTANCEMajor depressive disorder (MDD) exhibits a high comorbidity rate with irritable bowel syndrome (IBS). Our study, conducted on 120 MDD patients (47 of whom were comorbid with IBS) and a control group of 70 individuals, revealed that MDD-IBS comorbid patients demonstrated significantly higher depression/anxiety scores. Multi-omics analysis indicated substantial alterations in the gut microbiota (e.g., Firmicutes, Actinobacteria) and serum metabolites (e.g., bile acids, glyceric acid) among MDD-IBS patients, which were associated with specific metabolic pathways. Therefore, the new aspect of this study was the inclusion of patients with MDD but without IBS symptoms, which provided a deeper understanding of the intestinal microbiota dysregulation associated with comorbid IBS and MDD. These findings suggest that there may be involvement of the gut-brain axis, providing new research directions for potential therapeutic targets.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2100041598.}, } @article {pmid41043307, year = {2025}, author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q}, title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.}, journal = {International dental journal}, volume = {75}, number = {6}, pages = {103929}, pmid = {41043307}, issn = {1875-595X}, mesh = {Animals ; *Dysbiosis/etiology/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/physiology ; Mice ; *Neuroinflammatory Diseases/etiology/metabolism ; *Tooth Loss/complications ; Male ; *Neurons/drug effects ; Disease Models, Animal ; }, abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.

METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-α) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.

RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.

CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.

CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.}, } @article {pmid41033498, year = {2026}, author = {Saejung, C and Akkahat, S}, title = {Light color-based proliferation of purple phototrophic bacteria in a microbial consortium for sustainable wastewater treatment and bioproduct generation.}, journal = {Bioresource technology}, volume = {440}, number = {}, pages = {133411}, doi = {10.1016/j.biortech.2025.133411}, pmid = {41033498}, issn = {1873-2976}, mesh = {*Wastewater/microbiology ; *Microbial Consortia/radiation effects/physiology ; *Light ; Color ; *Water Purification/methods ; Biomass ; Biological Oxygen Demand Analysis ; Rhodopseudomonas/metabolism/growth & development ; }, abstract = {Purple phototrophic bacteria (PPB) offer distinct advantages for wastewater treatment. However, the application of pure cultures of PPB in large-scale wastewater treatment is constrained by isolation challenges and microbial competition. Therefore, we investigated light color treatment as a tool to enrich PPB within a natural microbial consortium for integrated wastewater treatment and bioproduct generation. We used metagenomics to assess PPB population dynamics and measured bioproduct yields of pigments, protein, biomass, and polyhydroxybutyrate as well as chemical oxygen demand removal (COD). While an initial enrichment yielded low PPB abundance (12 %), subsequent exposure to specific light color greatly altered the community composition. White light (465 nm) enriched the consortium with 76 % PPB abundance, dominated by Rhodopseudomonas sp., which maximized bacterial biomass, polyhydroxybutyrate accumulation, and COD removal. Conversely, red light (616 nm) suppressed PPB proliferation but enhanced specific yields of photosynthetic pigments and protein, indicating a metabolic trade-off between growth and bioproduction. Thus, light color treatment may be a simple and powerful strategy to boost PPB abundance and performance within a microbial consortium, creating a cost-effective platform for wastewater biorefineries.}, } @article {pmid40996271, year = {2025}, author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.}, journal = {mBio}, volume = {16}, number = {11}, pages = {e0190425}, pmid = {40996271}, issn = {2150-7511}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; *Microbial Consortia ; Metagenomics ; Bacteroides ; Female ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Male ; Bacteria/classification/genetics/isolation & purification ; Akkermansia ; }, abstract = {Composition and function of the gut microbiome are associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models in recapitulating ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure, and their ecological features were compared to human donors by metagenomic sequencing. HMA mice resembled other mice more than their respective human donors in gut microbial composition and function, with taxa including Akkermansia muciniphila and Bacteroides spp. enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse data sets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice was more like other mice than their human donor. Our data suggest that HMA mice are limited models for assessing the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overshadow ecological effects of treatments in humans that HMA models aim to recapitulate.IMPORTANCEHMA mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effects of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, Microbial Ecosystem Therapeutic 4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbor a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.}, } @article {pmid40980884, year = {2025}, author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG}, title = {Hi-C-resolved metagenomics reveals host range variation among mobile genetic elements within the European honey bee.}, journal = {mBio}, volume = {16}, number = {11}, pages = {e0224325}, pmid = {40980884}, issn = {2150-7511}, support = {//Project Apis m. (PAm)/ ; 2005306//National Science Foundation/ ; 2022049//National Science Foundation/ ; }, mesh = {Animals ; Bees/microbiology ; *Metagenomics/methods ; *Interspersed Repetitive Sequences ; *Host Specificity/genetics ; Bacteriophages/genetics ; Metagenome ; Phylogeny ; Plasmids/genetics ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; }, abstract = {Mobile genetic elements (MGEs), such as plasmids and bacteriophages, are major contributors to the ecology and evolution of host-associated microbes due to symbiotic interactions and gene flow via horizontal gene transmission. Antibiotic resistance genes (ARGs), which are frequently trafficked via MGEs, are known to be enriched within North American honey bee microbiomes due to decades of antibiotic exposure. While previous studies have identified nearly identical MGE-associated ARGs across geographically disparate honey bee colonies, our understanding of how ARGs are distributed and mobilized within and between individual microbiomes is limited. To address this limitation, we leverage Hi-C-resolved metagenomics with the honey bee worker gut microbiome and show that the worker gut contains dense, nested, and highly distinct MGE communities. We show that phage-microbe networks exhibit high variation among individual metagenomes and that phages show broad host range with respect to both the number and phylogenetic distance of their hosts. Comparisons of individual microbiomes reveal highly individualized plasmid communities that exhibit broad host range variation within microbiomes. Finally, we provide specific evidence that antibiotic resistance cassettes are being actively shuttled between honey bee microbes via plasmids and that these broad host range plasmids frequently recombine to share gene content. Our work corroborates early observations of ARG dispersal in honey bee colonies and provides evidence for how these genes are mobilized within and across honey bee-associated microbial communities.IMPORTANCEMobile genetic elements (MGEs) are found in every microbial community and often encode genes conferring antibiotic resistance (ARGs). Within the honey bee worker gut microbiome, ARGs are particularly frequent due to decades of antibiotic exposure. Previous studies have identified nearly identical ARGs in geographically disparate honey bee colonies, which suggests recent mobilization by MGEs into these colonies, but identifying how these ARGs are mobilized and distributed within honey bee colonies remains a challenging task, as most techniques rely on microbial culture. Applying metagenomic Hi-C, we describe how these ARGs are distributed among individual plasmid backbones and how those plasmids are distributed among host microbial populations. Remarkably, we find plasmids exhibit broad host range variation, although they encode nearly identical ARGs. Our work corroborates earlier observations of ARG dispersal in honey bee colonies and provides further evidence for how these ARGs are mobilized across vast geographic distance.}, } @article {pmid40961576, year = {2026}, author = {Sun, H and Guo, X and Sun, J and Zhou, W and Yu, Z and Li, M and Zhang, S and Liu, X and Zhao, Y and Zhang, Y}, title = {Metagenome assembled genomes revealed the influences of mariculture and seagrass species on the microbiomes in seawater and rhizosphere biotopes.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 1}, pages = {118703}, doi = {10.1016/j.marpolbul.2025.118703}, pmid = {40961576}, issn = {1879-3363}, mesh = {*Rhizosphere ; *Seawater/microbiology ; *Microbiota/genetics ; *Metagenome ; Bacteria/genetics/classification ; *Alismatales ; }, abstract = {Seagrasses provide critical ecosystem services, with their associated microbiomes playing vital roles in the health and adaptation of hosts. Metagenome sequencing has significantly advanced our understanding of seagrass-associated microbiomes; however, the application and interpretive reliability of metagenome-assembled genomes (MAGs) remain limited. This study presented a comparative analysis of high-quality MAGs from seawater and rhizosphere samples across five distinct marine habitats. A total of 93 dereplicated high-quality MAGs were obtained from seawater and rhizosphere samples and assigned to 5 and 11 phyla, respectively. Rhizosphere-derived MAGs were predominated by Desulfobacterota and exhibited enriched genes for carbon/nitrogen metabolism, dissimilatory sulfate reduction/oxidation, and glycopeptide antibiotic resistance. In contrast, MAGs from seawater primarily belonged to Pseudomonadota and Bacteroidota, with enriched genes in assimilatory sulfate reduction pathway and fluoroquinolone/tetracycline antibiotic resistance. Statistical analysis revealed that oyster culture had significantly elevated gene abundance of MAG functions linked to carbon metabolism, dissimilatory nitrate reduction, and nitrogen fixation processes in rhizosphere, while differences between seagrass species were minimal. Additionally, environmental factors, such as total organic carbon concentrations and particle sizes, exhibited closer interactions with functions of rhizosphere-associated MAGs compared to seawater samples. Our study provided novel insight into seagrass microbiome ecology, establishing a comparative genome-resolved framework to investigate functional adaptation of marine microbiome across distinct biotopes, and demonstrating the efficacy of MAG-based analysis for unrevealing environment-microbiome interactions in uncultured systems. These findings extend knowledge for developing microbial biomarkers of seagrass ecosystem health and offer methodological references for functional microbiome studies in coastal environments.}, } @article {pmid40957481, year = {2025}, author = {Ren, Y and Fang, H and Gao, Y and Yin, G and He, X and Chen, N}, title = {Effects of exercise on gut microbiota in older people with sarcopenia: Study protocol for a randomised controlled trial.}, journal = {Experimental gerontology}, volume = {211}, number = {}, pages = {112898}, doi = {10.1016/j.exger.2025.112898}, pmid = {40957481}, issn = {1873-6815}, mesh = {*Sarcopenia/therapy/microbiology/physiopathology ; Humans ; *Gastrointestinal Microbiome/physiology ; Aged ; Single-Blind Method ; *Resistance Training/methods ; Male ; Female ; Randomized Controlled Trials as Topic ; Quality of Life ; Animals ; Mice ; Muscle Strength ; Muscle, Skeletal ; }, abstract = {BACKGROUND: Sarcopenia is an age-related disease imposing a substantial burden on individuals and healthcare systems. Resistance training (RT) is recommended as the primary non-pharmacological treatment, and Baduanjin (BDJ) has shown positive effects for sarcopenia. However, the mechanisms through which exercise improves sarcopenia remain unclear. Research has suggested that exercise may enhance sarcopenia through the gut-muscle axis. Therefore, the present study aims to evaluate the effects of BDJ-RT on the gut microbiota in older people with sarcopenia, identify potential target microbial taxa and explore related mechanisms.

METHODS: In this 12-week randomised, single-blind controlled trial, 30 older people with sarcopenia will be randomly assigned to the BDJ-RT group (n = 15) or control group (n = 15). The BDJ-RT group will undergo BDJ combined with RT, and the control group will receive health education. Muscle mass, strength, physical performance, quality of life, gut microbiota and short-chain fatty acids will be assessed at baseline, post-intervention and follow-up. Potential target gut microbiota related to sarcopenia will be identified through metagenomic sequencing. The identified strains will then be gavaged to sarcopenic mice to evaluate their effects on sarcopenia. Data will be analysed using an intention-to-treat approach.

DISCUSSION: This study will be the first to systematically investigate the effects of BDJ-RT on the gut microbiota in older people with sarcopenia. The findings will provide potential microbial targets and mechanistic insights into the gut-muscle axis underlying exercise-induced improvements in sarcopenia.

TRIAL REGISTRATION: This study was registered on the International Traditional Medicine Clinical Trial Registry, with registration number ITMCTR2025000036.}, } @article {pmid40929372, year = {2025}, author = {Huereca, A and Allen, CCG and McMullin, RT and Simon, A and Belosokhov, A and Spribille, T}, title = {Evidence for extensive diversity in the pollen-parasitic genus Retiarius in western North America, including two new species associated with lichens.}, journal = {Mycologia}, volume = {117}, number = {6}, pages = {1148-1174}, doi = {10.1080/00275514.2025.2513197}, pmid = {40929372}, issn = {1557-2536}, mesh = {*Lichens/microbiology ; Phylogeny ; DNA, Fungal/genetics/chemistry ; North America ; *Pollen/microbiology ; *Ascomycota/genetics/classification/isolation & purification/cytology ; DNA, Ribosomal Spacer/genetics/chemistry ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Molecular Sequence Data ; Canada ; *Biodiversity ; }, abstract = {Understanding the diversity of microscopic hyphomycetes is an ongoing effort, and many species remain undescribed. While studying lichen organismal composition in western Canada, metagenomic data revealed the presence of an unknown species of Retiarius (Orbiliaceae, Ascomycota), a genus of pollen-parasitic fungus with no previous records in the region. We developed genus-specific primers to amplify Retiarius DNA in lichen and adjacent substrate extractions, successfully detecting multiple lineages of Retiarius across a wide geographic range within North America. We proceeded to screen accumulations of pollen on the undersurface of lichen thalli to isolate any pollen-associated fungi. Using dilution series and PCR for identification, we isolated two specifically distinct strains of Retiarius with morphology unlike any described member of the genus. Inclusion of DNA from these strains in a multilocus phylogeny using the internal transcribed spacer regions ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and nuc small subunit (18S) confirmed their evolutionarily distinct position in the genus. We describe these two species here as Retiarius canadensis and R. crescentus. The former possesses trinacrium-shaped conidia, similar to those of R. bovicornutus and R. revayae but morphometrically different, and the latter is distinguished by its canoe-shaped conidia, a morphological character heretofore unknown from Retiarius.}, } @article {pmid40902606, year = {2025}, author = {Zhang, D and Zou, Y and Shi, Y and Zhang, J and Liu, J and Wu, G and Zhang, J and Gao, Y and Chen, M and Li, YX}, title = {Systematically investigating and identifying bacteriocins in the human gut microbiome.}, journal = {Cell genomics}, volume = {5}, number = {11}, pages = {100983}, doi = {10.1016/j.xgen.2025.100983}, pmid = {40902606}, issn = {2666-979X}, mesh = {Humans ; *Bacteriocins/genetics/biosynthesis/metabolism/pharmacology ; *Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/metabolism ; Feces/microbiology ; }, abstract = {Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.}, } @article {pmid40845582, year = {2025}, author = {Li, Y and Zhang, C and Meng, Z and You, M and Shi, H}, title = {Microbial dysbiosis induced in Cyprinus carpio by tetrabromobisphenol A exposure: Mediation through gut barrier impairment and oxidative stress.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {56}, number = {}, pages = {101609}, doi = {10.1016/j.cbd.2025.101609}, pmid = {40845582}, issn = {1878-0407}, mesh = {Animals ; *Carps/microbiology ; *Oxidative Stress/drug effects ; *Dysbiosis/chemically induced/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Polybrominated Biphenyls/toxicity ; *Water Pollutants, Chemical/toxicity ; *Fish Diseases/microbiology/chemically induced ; }, abstract = {The frequent detection of Tetrabromobisphenol A (TBBPA) in environmental media has elicited considerable scientific concern. The ecotoxicological impacts of TBBPA on intestinal health in the common carp (Cyprinus carpio) were systematically investigated through integrated histopathological, biochemical, and metagenomic analyses. Fish were exposed to environmentally relevant TBBPA concentrations (0, 0.005, 0.05, and 0.5 mg/L) for a 14-day duration. Dose-dependent intestinal damage was induced by TBBPA exposure, manifested as villus fusion and atrophy, oxidative stress (diminished SOD/CAT activities and elevated MDA levels), and downregulated expression of tight junction proteins (ZO-1, Claudin-3, Occludin). This collectively compromised barrier integrity and triggered pro-inflammatory cytokine upregulation of TNF-α alongside anti-inflammatory IL-10 suppression. Significant intestinal microbial dysbiosis was detected via 16S rRNA sequencing. Alpha diversity indices were reduced at low concentrations (0.005 mg/L) of TBBPA but elevated at higher concentrations (0.05-0.5 mg/L). TBBPA exposure induced gut microbiota perturbations, characterized by depletion of beneficial taxa (Cetobacterium) and enrichment of opportunistic pathogens (Legionella and Thermomonas). Functional prediction analyses indicated that these microbial alterations may influence carbohydrate metabolism, and vitamin biosynthesis within the intestinal tract of common carp. Collectively, these findings demonstrated that TBBPA disrupted intestinal health via synergistic mechanisms involving oxidative stress, histopathological damage, and microbiota-mediated dysregulation. This investigation addresses a critical knowledge gap regarding the impacts of TBBPA on fish gut microbiota, while providing provided a reference for assessing the potential ecological risks of TBBPA in the environment.}, } @article {pmid40760050, year = {2025}, author = {Oh, J and Voigt, AY}, title = {The human skin microbiome: from metagenomes to therapeutics.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {12}, pages = {771-787}, pmid = {40760050}, issn = {1740-1534}, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *Metagenome ; Bacteria/genetics/classification ; Metagenomics ; Fungi/genetics ; Skin Microbiome ; }, abstract = {The skin microbiome is composed of a diverse community of microorganisms, including bacteria, fungi, viruses and mites. These microorganisms have a crucial role in maintaining skin health, protecting against pathogens and modulating immune responses. In recent years, our understanding of the skin microbiome has expanded substantially with the deployment of metagenomic sequencing. This technology, by reconstructing microbial species, strains and gene pathways in the microbiomes of different cohorts, has led to identification of numerous therapeutic targets and thus propelled the development of therapeutic approaches that are aimed at leveraging these microorganisms to treat skin conditions and to improve skin health. In this Review, we discuss the composition, ecology, functions and therapeutic horizons of the human skin microbiome, presenting examples of studies that highlight potential therapeutic targets in the skin microbiome, ongoing progress in the development of skin microbiome-based therapeutics and challenges.}, } @article {pmid40751372, year = {2025}, author = {Bryant, JA and Straub, TJ and Pardi, DS and Litcofsky, KD and Kelly, CR and Chafee, ME and Cohen, SH and Khanna, S and Berenson, CS and Wortman, J and Sims, M and Ford, CB and Lombardo, MJ and McGovern, BH and von Moltke, L and Kraft, CS and Henn, MR and Hasson, BR}, title = {Comparability of Gastrointestinal Microbiome and Bile Acid Profiles in Patients With First or Multiply Recurrent Clostridioides difficile Infection.}, journal = {The Journal of infectious diseases}, volume = {232}, number = {5}, pages = {e733-e740}, doi = {10.1093/infdis/jiaf408}, pmid = {40751372}, issn = {1537-6613}, support = {//Seres Therapeutics/ ; }, mesh = {Humans ; *Bile Acids and Salts/analysis/metabolism ; *Gastrointestinal Microbiome ; *Clostridium Infections/microbiology/drug therapy/therapy ; Male ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Clostridioides difficile ; Aged ; Recurrence ; Anti-Bacterial Agents/therapeutic use ; Adult ; Fecal Microbiota Transplantation ; }, abstract = {BACKGROUND: Clostridioides difficile infection (CDI) treatment guidelines suggest varied approaches for patients with first (frCDI) or multiply recurrent CDI (mrCDI). Low microbial diversity, elevated primary bile acids (BA), and low secondary BA concentrations favor germination of C. difficile spores into toxin-producing bacteria and are believed to increase rCDI risk. Greater understanding of the gastrointestinal (GI) microbiome in rCDI may inform management of the disease. We describe a post hoc comparison of GI microbiome and bile acid profiles between patients with frCDI and mrCDI in a Phase 3 open-label trial, ECOSPOR IV, of fecal microbiota spores, live-brpk (VOWST®; VOS, formerly SER-109), an orally-administered live microbiome therapeutic.

METHODS: Patients received VOS following symptom resolution after standard-of-care antibiotics. Pretreatment baseline (within 3 days following antibiotic completion) and Week 1 post-dosing stool samples were collected for whole metagenomic sequencing and metabolomics. Diversity was calculated from MetaPhlAn2 species profiles. Concentrations of primary and secondary BAs were measured via targeted LC-MS/MS.

RESULTS: rCDI rates through Week 8 were similarly low in both frCDI and mrCDI patients (6.5% versus 9.7%, respectively). Baseline microbial diversity was similarly low between frCDI and mrCDI subgroups (P > .05). Diversity and secondary BA concentrations increased in both subgroups, whereas primary BA concentrations declined following VOS dosing, leading to few differences between subgroups at Week 1.

CONCLUSIONS: These data suggest commonalities in microbiome disruption in patients with frCDI and mrCDI that contribute to recurrence and suggest that antibiotics followed by a live microbiome therapy may be an optimal treatment strategy for rCDI, regardless of number of prior CDI recurrences.}, } @article {pmid41222645, year = {2025}, author = {Rana, S and Das, KK and Singh, SK and Bhattacharyya, D}, title = {Deciphering Fungal Communities in Three Species of Phlogacanthus Nees (Acanthaceae) Using Amplicon-Metagenomic Analysis.}, journal = {Current microbiology}, volume = {83}, number = {1}, pages = {16}, pmid = {41222645}, issn = {1432-0991}, abstract = {Fungal communities play vital roles in plant health, nutrient cycling, and ecological balance. Species of Phlogacanthus Nees, valued for their medicinal and ecological importance, harbor diverse fungal microbiomes that may influence growth, resilience, and metabolite production. This study investigated fungal communities associated with three Phlogacanthus species-P. tubiflorus Nees (SKS-1), P. thyrsiformis (Roxb. ex Hardw.) Mabb. (SKS-2), and P. curviflorus (Wall.) Nees (SKS-3)-using high-throughput amplicon-metagenomic sequencing of the ITS2 region on the Illumina MiSeq platform. A total of 153 operational taxonomic units (OTUs) were identified, with SKS-2 showing the highest richness (129 OTUs), followed by SKS-1 (112) and SKS-3 (95). Seventy OTUs were shared across all species, while 10, 22, and 8 were unique to SKS-1, SKS-2, and SKS-3, respectively. Alpha diversity indices (Chao1, ACE, Shannon, Simpson, Inverse Simpson, Fisher's alpha) confirmed SKS-2 as the most species-rich fungal habitat. A high proportion of unclassified taxa in SKS-2, along with dominance of Pleosporales, suggests the presence of novel fungi with ecological and biotechnological significance. Beta diversity analysis using Bray-Curtis dissimilarity and Principal Coordinate Analysis revealed significant differences among the fungal communities of the three species. Overall, SKS-2 emerged as the most diverse habitat, while SKS-3 supported a unique but less diverse assemblage. This is the first report profiling fungal microbiomes of Phlogacanthus species. The results highlight their potential as reservoirs of endophytes with applications in plant growth promotion, stress tolerance, biocontrol, enzyme production, and bioactive metabolite discovery, offering leads for sustainable agriculture and biotechnology.}, } @article {pmid41217690, year = {2025}, author = {Nguyen, HN and Kim, OTP and Tran, TT}, title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {11}, pages = {445}, pmid = {41217690}, issn = {1573-0972}, support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; }, mesh = {*Honey/microbiology ; Vietnam ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; *Virulence Factors/genetics ; *Metagenomics/methods ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Bacterial/genetics ; Bees/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Genes, Bacterial ; Virulence/genetics ; }, abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.}, } @article {pmid41211940, year = {2025}, author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ}, title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70101}, pmid = {41211940}, issn = {1529-8817}, support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; }, abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.}, } @article {pmid41147939, year = {2025}, author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Ai, L and Zhang, Z and Xie, F}, title = {Docynia delavayi (Franch.) Schneid polyphenols alleviate dextran sulfate sodium-induced colitis by regulating the gut microbiota.}, journal = {Food & function}, volume = {16}, number = {22}, pages = {8846-8861}, doi = {10.1039/d5fo03604f}, pmid = {41147939}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Dextran Sulfate/adverse effects ; *Colitis/chemically induced/drug therapy/microbiology ; *Polyphenols/pharmacology/administration & dosage/chemistry ; Mice ; Male ; Anti-Inflammatory Agents/pharmacology ; Mice, Inbred C57BL ; *Plant Extracts/pharmacology/chemistry/administration & dosage ; Disease Models, Animal ; Cytokines/metabolism ; Humans ; }, abstract = {Docynia delavayi (Franch.) Schneid is rich in polyphenols; however, its functions remain unclear. In this study, we identified and characterized the key constituents of D. delavayi fruit polyphenols (DDP), validated their anti-inflammatory effects, and provided insights into their underlying mechanisms of action. UPLC-MS/MS was used to quantify the major phenolic compounds in DDP, including glycitin, procyanidin B2, vitexin, myricitrin, astilbin, chlorogenic acid, phlorizin, (-)-epicatechin, naringenin-7-O-glucoside, taxifolin-7-O-rhamnoside, rhoifolin, methylnissolin-3-O-glucoside, and scutellarein. In the dextran sulfate sodium-induced colitis mouse model, DDP significantly improved colon length and the disease activity index. It also reduced the expression of inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α. Metagenomic analysis revealed that DDP increased gut microbiota diversity, particularly enriching species capable of producing short-chain fatty acids (SCFAs), such as Lawsonibacter and Ruminiclostridium. Metabolomic data further demonstrated the upregulation of SCFA-associated pathways, such as glycolysis and pyruvate metabolism, with elevated colonic acetate, propionate, and butyrate levels corroborating these findings. Multi-omics analysis linked SCFAs to reduced inflammation. Collectively, these findings suggest that SCFAs play a pivotal role in the anti-inflammatory effects of DDP by modulating the gut microbiota to enhance SCFA biosynthesis. These findings demonstrate that SCFAs serve as critical mediators of the anti-inflammatory properties of DDP, highlighting their considerable potential as natural therapeutic agents for intestinal inflammation.}, } @article {pmid41075335, year = {2025}, author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF}, title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.}, journal = {Research in veterinary science}, volume = {196}, number = {}, pages = {105930}, doi = {10.1016/j.rvsc.2025.105930}, pmid = {41075335}, issn = {1532-2661}, mesh = {Alberta ; Animals ; *Microbiota ; *Housing, Animal ; *Air Microbiology ; *Chickens/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/isolation & purification ; Air Pollution, Indoor ; }, abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.}, } @article {pmid41060313, year = {2025}, author = {Hays, MD and Fuchsman, CA}, title = {SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41060313}, issn = {1751-7370}, support = {//Horn Point Laboratory/ ; }, mesh = {*Ecotype ; *Seawater/microbiology/chemistry ; Phylogeny ; Oceans and Seas ; *Light ; *Oxygen/metabolism ; *Bacteria/classification/genetics ; Phytoplankton ; Cyanobacteria ; }, abstract = {SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smaller ecotypes inhabit different ecological niches. Using metagenomic read placement onto a phylogenetic tree of RNA polymerase (rpoB), we were able to determine the distribution of different ecotypes both geographically and by depth. Our method avoids biases from the absence of quality sequenced genomes for deep SAR11 ecotypes. Depth profiles that range from the surface to the bathypelagic were analyzed at 30 stations in six ocean basins. In the euphotic zone, changes in the dominant primary producer from eukaryotic algae to cyanobacteria, did not cause the abundance of SAR11 to shift between stations. However, specific SAR11 ecotypes did correlate with eukaryotic phytoplankton (1a.3 and 1a.4) or picocyanobacteria (1b.2, 1b.4, and IIaB). In the lower euphotic and mesopelagic zones, group IIb.x was overwhelmingly the dominant species but group 1c was also present, and we found several new deep subecotypes of 1b. The shift between the surface SAR11 community, dominated by 1a and surface 1b subecotypes, and the mesopelagic ecotype groups, corresponded to the maximum decrease in the light-dependent proteorhodopsin/rpoB ratio, indicating that many deep ecotypes did not possess proteorhodopsin. This ecotype switch repeatedly corresponded to the maximum in Low Light I Prochlorococcus, leading to the hypothesis that changes in light motivates the ecotype switch. Environmentally abiotic factors like light and temperature appear to be determining factors in the SAR11 ecotype distribution throughout the global oceans.}, } @article {pmid41060304, year = {2025}, author = {Bueno de Mesquita, CP and Olm, MR and Bissett, A and Fierer, N}, title = {High strain-level diversity of Bradyrhizobium across Australian soils.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41060304}, issn = {1751-7370}, support = {//Bioplatforms Australia and the Integrated Marine Observing System/ ; //Australian Government's National Collaborative Research Infrastructure Strategy/ ; //Australian Government/ ; //BHP/ ; //CSIRO/ ; //Novo Nordisk Foundation/ ; //U.S. National Science Foundation/ ; //U.S. Army Research Office/ ; }, mesh = {*Bradyrhizobium/genetics/classification/isolation & purification ; *Soil Microbiology ; Australia ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Metagenome ; *Genetic Variation ; Soil/chemistry ; *Biodiversity ; }, abstract = {Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here, we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.}, } @article {pmid41026097, year = {2025}, author = {Patyka, M and Wang, R and Honchar, A and Patyka, T and Khablak, S}, title = {Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {11}, pages = {}, pmid = {41026097}, issn = {1574-6941}, mesh = {*Triticum/microbiology/growth & development ; *Rhizosphere ; *Bacillus subtilis/physiology ; *Microbiota ; *Soil Microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Indoleacetic Acids/metabolism ; Plant Roots/microbiology ; Phenotype ; }, abstract = {The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in aboveground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.}, } @article {pmid40915037, year = {2025}, author = {Baud, D and Peric, A and Vidal, A and Weiss, JM and Engel, P and Das, S and Stojanov, M}, title = {Genital microbiota in infertile couples.}, journal = {Reproductive biomedicine online}, volume = {51}, number = {5}, pages = {105056}, doi = {10.1016/j.rbmo.2025.105056}, pmid = {40915037}, issn = {1472-6491}, mesh = {Humans ; Female ; Male ; *Microbiota ; *Vagina/microbiology ; *Infertility/microbiology ; Adult ; Semen/microbiology ; Follicular Fluid/microbiology ; Penis/microbiology ; }, abstract = {RESEARCH QUESTION: What is the composition of bacterial communities at various genital sites and are there potential interactions between partners' microbiota?

DESIGN: This observational study involved metagenomic analyses of samples collected from male and female partners of couples undergoing fertility treatment. Samples included vaginal and penile swabs, as well as follicular fluid and semen, which were analysed using next-generation sequencing.

RESULTS: The bacterial community profiles of different genital tract niches were distinct, niche-specific compositions, with female samples predominantly featuring Lactobacillus species and male samples displaying greater microbial diversity, including genital-specific and skin-associated taxa. Significant differences were observed between the sample types and intra-couple comparisons, which suggested potential microbiota interactions between partners. Differential abundance analyses further identified genera specifically enriched in female versus male samples, and correlations between partner samples point towards possible microbial transmission or shared influences on genital microbiota composition.

CONCLUSIONS: Despite advances in reproductive medicine, many infertility cases remain idiopathic, prompting exploration into how the genital microbiota (both in female and male reproductive tracts) might influence reproductive success. Our findings reveal that, although female samples were predominantly colonized by Lactobacillus species, particularly in the lower genital tract, male samples had greater microbial diversity (including bacteria linked to bacterial vaginosis), with only limited evidence of inter-partner microbiota transmission, underscoring the need for further longitudinal studies on the effect of sexual activity on microbial dynamics.}, } @article {pmid40902732, year = {2025}, author = {Blecksmith, SE and Oliver, A and Alkan, Z and Lemay, DG}, title = {Gut Microbiome Genes Involved in Plant and Mucin Breakdown Correlate with Diet and Gastrointestinal Inflammation in Healthy United States Adults.}, journal = {The Journal of nutrition}, volume = {155}, number = {11}, pages = {3757-3768}, doi = {10.1016/j.tjnut.2025.08.027}, pmid = {40902732}, issn = {1541-6100}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adult ; Male ; Female ; United States ; *Diet ; *Mucins/metabolism ; *Inflammation/microbiology ; Dietary Fiber/administration & dosage ; Middle Aged ; Feces/microbiology ; *Plants/metabolism ; }, abstract = {BACKGROUND: Dietary carbohydrates shape the composition and function of gut microbes, which may potentially influence human health. It is not known if these diet-microbiome relationships are relevant to healthy American adults.

OBJECTIVES: We hypothesized that intake of dietary fiber by healthy adults would be associated with the carbohydrate-active enzyme (CAZyme) capacity of their gut microbiome and that this capacity would be negatively correlated with gastrointestinal (GI) inflammation.

METHODS: We analyzed dietary data, GI inflammation, and CAZyme profiles from shotgun metagenomes of fecal samples in the US Department of Agriculture (USDA) Nutritional Phenotyping Study cohort of healthy United States adults (n = 330).

RESULTS: CAZyme diversity varied across participants. Plant CAZyme diversity and abundance correlated significantly with fecal pH (Shannon: adjusted R[2] = 0.053, P < 0.001; Chao1: adjusted R[2] = 0.056, P < 0.001; abundance: adjusted R[2] = 0.036, P < 0.001) and habitual energy-adjusted total fiber (Shannon: adjusted R[2] = 0.015, P = 0.029; abundance: adjusted R[2] = 0.015, P = 0.010) and soluble fiber intake (Shannon: adjusted R[2] = 0.017, P = 0.019; abundance: adjusted R[2] = 0.015, P = 0.0010). The ratio of mucin-degrading CAZymes to plant-degrading enzymes, coined here as the metric Muc2Plant, varied across participants and differed by sex (Wilcoxon, P = 0.035) and body mass index (adjusted R[2] = 0.028, P = 0.017). Muc2Plant positively correlated with GI inflammation (calprotectin: adjusted R[2] = 0.038, P = 0.001; neopterin: adjusted R[2] = 0.071, P < 0.001). Machine learning (ML) classification models were used to identify specific foods (e.g., potatoes) and microbes (e.g., Lachnospiraceae) as predictors of low Muc2Plant.

CONCLUSIONS: These results support the relevance of diet-microbiome relationships even in healthy adults, and that reduction of Muc2Plant, via dietary and/or microbial interventions, would be a beneficial health target to potentially prevent dysbiosis and reduce GI inflammation. This trial was registered at clinicaltrials.gov as NCT02367287.}, } @article {pmid40709814, year = {2025}, author = {Labisa-Morais, F and Valente, D and Blanco-Míguez, A and Manghi, P and Garcia-Valiente, A and Andriamaniraka, H and Armanini, F and Asnicar, F and De Gregorio, C and Golzato, D and Manara, S and Modesto, M and Piperni, E and Punčochář, M and Scarafile, D and Torti, V and Borruso, L and Mattarelli, P and Giacoma, C and Sandri, C and Spiezio, C and Segata, N and Valles-Colomer, M}, title = {Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40709814}, issn = {1751-7370}, support = {BG22/00172//Spanish Ministry of Universities to MV-C/ ; PID2022-139328OA-I00//Knowledge Generation Project/ ; ERC-CoG microTOUCH-101045015/ERC_/European Research Council/International ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Lemur/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Metagenome ; Endangered Species ; Female ; Social Behavior ; Social Group ; }, abstract = {The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri fecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.}, } @article {pmid41206740, year = {2025}, author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP}, title = {A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf056}, pmid = {41206740}, issn = {1574-6976}, abstract = {100 years after Planctomycetes were discovered and fifty years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in over 150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of Planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to bee revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of Planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of Planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a great potential of biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in Planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to Planctomycetes and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.}, } @article {pmid41204634, year = {2025}, author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q}, title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.}, journal = {Journal of food science}, volume = {90}, number = {11}, pages = {e70654}, doi = {10.1111/1750-3841.70654}, pmid = {41204634}, issn = {1750-3841}, support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactobacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; }, abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.}, } @article {pmid41203618, year = {2025}, author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M}, title = {Development of the preterm infant gut and gastric residuals microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9848}, pmid = {41203618}, issn = {2041-1723}, mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; }, abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.}, } @article {pmid41202544, year = {2025}, author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X}, title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140322}, doi = {10.1016/j.jhazmat.2025.140322}, pmid = {41202544}, issn = {1873-3336}, abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.}, } @article {pmid41201920, year = {2025}, author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ}, title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.}, journal = {Neoplasia (New York, N.Y.)}, volume = {70}, number = {}, pages = {101245}, doi = {10.1016/j.neo.2025.101245}, pmid = {41201920}, issn = {1476-5586}, mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; }, abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.}, } @article {pmid41201839, year = {2025}, author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F}, title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).}, journal = {Microbial genomics}, volume = {11}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001541}, pmid = {41201839}, issn = {2057-5858}, mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; }, abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.}, } @article {pmid41201223, year = {2025}, author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q}, title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {5}, pages = {37069}, doi = {10.31083/IJVNR37069}, pmid = {41201223}, issn = {0300-9831}, support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; }, abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.}, } @article {pmid41199348, year = {2025}, author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N}, title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {227}, pmid = {41199348}, issn = {2049-2618}, support = {ANR-11-DPBS-0001//Metagenopolis/ ; }, mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; }, abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.}, } @article {pmid41198823, year = {2025}, author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, Ó}, title = {The association of the rumen virome with methane emissions in dairy cattle.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1534}, pmid = {41198823}, issn = {2399-3642}, mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; }, abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.}, } @article {pmid40815091, year = {2025}, author = {Garcia-Pichel, F and Farias, J and Fernandes, V and Roush, D and Swenson, TL and Kosina, SM and Northen, TR and Cao, H and Jaunin, S and Kandel, R and Gaxiola, R}, title = {Swift microbiome-mediated phenotype transfer from transgenic plants.}, journal = {Journal of environmental quality}, volume = {54}, number = {6}, pages = {1368-1382}, doi = {10.1002/jeq2.70070}, pmid = {40815091}, issn = {1537-2537}, mesh = {*Plants, Genetically Modified/microbiology ; *Arabidopsis/microbiology/genetics/physiology ; *Microbiota ; Phenotype ; Plant Roots/microbiology ; Soil Microbiology ; Butylene Glycols/metabolism ; }, abstract = {The expression of an organism's genes determines its own characteristics in any given environment. In this study, we demonstrate that the phenotypic traits of genetically modified transgenic Arabidopsis thaliana plants, designed for nutrient efficiency and enhanced yield, can be naturally and readily transferred to neighboring wild-type plants. Our findings reveal that the transgenic plants significantly influence the populational, compositional, and functional traits of their root-associated microbiome (RAM), resulting in a larger population, with distinct composition and high functional potential compared to wild-type plants, regardless of soil type. This phenomenon appears to stem from altered metabolite exudation patterns, which enhance root recruitment. Notably, the RAM plays a dual role: it not only contributes to the robust phenotype of the transgenic plants but also facilitates the transfer of these traits to adjacent wild-type plants. Upon transplanting wild-type plants into the presence of transgenics, we observed the induction of transgenic-like phenotypes. Metagenomic and compositional analyses indicate that this transfer is linked to an increase in 2,3-butanediol (2,3-BD) fermenting bacteria. Furthermore, exposure to 2,3-BD alone was sufficient to elicit transgenic phenotypes in wild-type plants. These results suggest that factors external to plant tissues, such as root-associated bacteria and their volatile metabolic products, play a crucial role in the transferability of plant phenotypes to neighboring plants. Our findings underscore the importance of evaluating microbiome interactions in the context of transgenic organisms and open new avenues for alternative agricultural practices that may reduce reliance on genetic modification.}, } @article {pmid41195309, year = {2025}, author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F}, title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.}, journal = {Pediatric diabetes}, volume = {2025}, number = {}, pages = {3013063}, pmid = {41195309}, issn = {1399-5448}, mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; }, abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.

METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included α/β-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.

RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2] = 0.0562, p=0.003 and R [2] = 0.0343, p=0.003). HLA-C [∗] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2] = 0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2] = 0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [∗] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19 ± 0.14 vs. 0.26 ± 0.19 µg/mL, p=0.029).

CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [∗] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.}, } @article {pmid41194562, year = {2025}, author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A}, title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70199}, doi = {10.1111/1462-2920.70199}, pmid = {41194562}, issn = {1462-2920}, support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnología/ ; }, mesh = {*Archaea/genetics/metabolism/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.}, } @article {pmid41194219, year = {2025}, author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH}, title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {136}, pmid = {41194219}, issn = {2524-6372}, support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; }, abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.

RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.

CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.}, } @article {pmid41183096, year = {2025}, author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ}, title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.}, journal = {PLoS pathogens}, volume = {21}, number = {11}, pages = {e1013667}, pmid = {41183096}, issn = {1553-7374}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/virology/immunology ; Immunocompromised Host ; Aged ; Bacteria/isolation & purification/genetics ; Microbiota ; Coinfection/microbiology ; Lung/microbiology/virology ; }, abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.}, } @article {pmid41192488, year = {2025}, author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y}, title = {Microbial necromass analogues reshape composting humification pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {133583}, doi = {10.1016/j.biortech.2025.133583}, pmid = {41192488}, issn = {1873-2976}, abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.}, } @article {pmid41189709, year = {2025}, author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J}, title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1619059}, pmid = {41189709}, issn = {2235-2988}, mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation & purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; }, abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.

METHODS: We recruited 91 participants, including 31 treatment-naïve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.

RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in α-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.

DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.}, } @article {pmid41189414, year = {2025}, author = {Zheng, Z and Zhao, L and Liu, Y and Wang, W and Zheng, K and Chen, X and Zhang, S and Sun, Y and Ma, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M and Gao, C and Sun, L and Liang, Y}, title = {Identification and Genomic Analysis of a New Viral Species With Low Similarity to Existing Viruses.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70201}, doi = {10.1111/1462-2920.70201}, pmid = {41189414}, issn = {1462-2920}, support = {LSKJ202203201//Laoshan Laboratory/ ; 42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions/ ; 2025M770867//China Postdoctoral Science Foundation/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Genome, Viral ; Metagenomics ; *Bacteriophages/genetics/isolation & purification/classification ; Phylogeny ; *Pseudoalteromonas/virology ; Genomics ; *Viruses/genetics/classification/isolation & purification ; }, abstract = {Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.}, } @article {pmid41188680, year = {2025}, author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA}, title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).}, journal = {Environmental geochemistry and health}, volume = {47}, number = {12}, pages = {547}, pmid = {41188680}, issn = {1573-2983}, support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; }, mesh = {*Geologic Sediments/microbiology ; *Biofilms ; Mining ; *Microbiota ; Metagenomics ; *Water Microbiology ; Western Australia ; Water Pollutants, Chemical/analysis ; Zinc/analysis ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.}, } @article {pmid41188618, year = {2025}, author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S}, title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {12}, pages = {1295}, pmid = {41188618}, issn = {1573-2959}, support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; }, mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; }, abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.}, } @article {pmid41081627, year = {2025}, author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M}, title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.}, journal = {Microbiology spectrum}, volume = {13}, number = {11}, pages = {e0173025}, pmid = {41081627}, issn = {2165-0497}, support = {ZY2022018//WMSTB | Science and Technology Plan Project of Wenzhou Municipality ()/ ; }, mesh = {Humans ; *Pterygium/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Conjunctiva/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Male ; Female ; Middle Aged ; Aged ; Virulence Factors/genetics ; Adult ; Dysbiosis/microbiology ; }, abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.}, } @article {pmid41069107, year = {2025}, author = {Ozel, B and Agirman, B and Simsek, O and Erten, H}, title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.}, journal = {Yeast (Chichester, England)}, volume = {42}, number = {11}, pages = {222-234}, doi = {10.1002/yea.70003}, pmid = {41069107}, issn = {1097-0061}, support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; }, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Yeasts/classification/genetics/metabolism/isolation & purification ; Hydrogen-Ion Concentration ; *Biodiversity ; Temperature ; Food Microbiology ; *Fermented Foods/microbiology ; *Bread/microbiology/analysis ; }, abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.}, } @article {pmid41025824, year = {2025}, author = {Li, Z and Li, S and Han, C and Chen, Y and Zhen, H and Sun, Y and Zhou, X and Chen, Y and Zheng, Y and Han, L and Krutmann, J and Nie, C and Wang, J and Xia, J}, title = {A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.}, journal = {Microbiology spectrum}, volume = {13}, number = {11}, pages = {e0117825}, pmid = {41025824}, issn = {2165-0497}, mesh = {Humans ; *Skin/virology/microbiology ; *Virome/genetics ; Microbiota/genetics ; *Viruses/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation & purification ; *DNA, Viral/genetics ; Metagenomics ; }, abstract = {UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem.

IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.}, } @article {pmid41025799, year = {2025}, author = {Buckner, AM and Glendinning, L and Palma Hidalgo, JM and van Munster, JM and Stevens, M and Watson, M and Newbold, CJ}, title = {The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.}, journal = {Microbiology spectrum}, volume = {13}, number = {11}, pages = {e0056325}, pmid = {41025799}, issn = {2165-0497}, support = {BB/T00875X/1, BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; UKSBS PR18037//Natural Environment Research Council/ ; }, mesh = {*Rumen/microbiology ; Animals ; *Bacteria/classification/isolation & purification/growth & development/genetics/metabolism ; *Culture Media/chemistry ; Anaerobiosis ; Methane/metabolism ; Gastrointestinal Microbiome ; Cattle ; Phylogeny ; }, abstract = {Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.}, } @article {pmid40996249, year = {2025}, author = {Luo, Y and Xu, X and Qiao, R and Zhao, R-P and Zhou, Z-W and Li, D-A and Wen, Y and Song, J-M and Chen, L-L}, title = {Comparative analysis of rhizosphere microbiomes of cultivated and wild rice under contrasting field water regimes.}, journal = {Microbiology spectrum}, volume = {13}, number = {11}, pages = {e0026325}, pmid = {40996249}, issn = {2165-0497}, mesh = {*Oryza/microbiology/growth & development ; *Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Water/metabolism ; Plant Roots/microbiology ; }, abstract = {UNLABELLED: Asian cultivated rice (Oryza sativa L.) is domesticated from the common wild rice (Oryza rufipogon Griff.). However, the increasing water stress caused by climate change in recent years has become a major threat to rice growth and yield. To explore the adaptive changes of rhizosphere microbiomes in annual cultivated and perennial wild rice under different water limitation conditions, we conducted metagenomic sequencing analysis on rice rhizosphere soil samples from natural environments with varying water conditions. In particular, the genus Pseudomonas plays a dominant role in the rhizosphere microbiome of wild rice under non-irrigated condition. For archaea, we found that, compared to non-irrigated condition, submergence condition enriched methanogenic Methanosarcina. In comparison to cultivated rice, wild rice showed significant enrichment of Nitrosarchaeum, as ammonia-oxidizing archaea play a key role in the nitrogen cycle, whereas cultivated rice tends to enrich methanogenic archaea (Methanosarcina), which may increase methane emissions and have adverse environmental impacts. The rhizosphere metabolites of wild rice also enriched DL-Norleucine, L-Phenylalanine, and Palmitic acid, which may enhance root water absorption and provide essential nutrients to help rice resist water-limiting stress. In terms of rhizosphere microbiome function, asnB and nirK were particularly enriched in wild rice under non-irrigated condition, suggesting that wild rice may exhibit higher ecological adaptability to water stress by enhancing nitrogen assimilation and denitrification processes. Excavating these microbiome communities and functional changes in rice rhizospheres is crucial for optimizing water-limiting resistance, protecting the environment, and improving rice yield.

IMPORTANCE: This study highlights the differences in rhizosphere microbiomes and metabolites between wild and cultivated rice, providing new insights into how water limitation impacts their interaction with the rhizosphere microbiome. These findings are crucial for advancing rice cultivation under submergence and non-irrigated conditions, offering strategies to optimize farming practices, manage water scarcity, and reduce methane emissions. In contrast to cultivated rice, wild rice may regulate its rhizosphere microbial community to enhance resistance to water stress. This discovery offers valuable theoretical support for improving rice growth and adaptation across diverse ecological environments.}, } @article {pmid41188334, year = {2025}, author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T}, title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38587}, pmid = {41188334}, issn = {2045-2322}, mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; }, abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.}, } @article {pmid41188324, year = {2025}, author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI}, title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38611}, pmid = {41188324}, issn = {2045-2322}, support = {NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; R37CA249007/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; }, abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.}, } @article {pmid41188219, year = {2025}, author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P}, title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9738}, pmid = {41188219}, issn = {2041-1723}, mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; }, abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.}, } @article {pmid41187070, year = {2025}, author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S}, title = {An Ocean of Opsins.}, journal = {Genome biology and evolution}, volume = {17}, number = {11}, pages = {}, doi = {10.1093/gbe/evaf189}, pmid = {41187070}, issn = {1759-6653}, support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; }, mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; }, abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.}, } @article {pmid41186205, year = {2025}, author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W}, title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {94}, number = {5}, pages = {e70178}, doi = {10.1111/aji.70178}, pmid = {41186205}, issn = {1600-0897}, support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; }, abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.

OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.

RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.

CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.}, } @article {pmid41185359, year = {2025}, author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y}, title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117622}, doi = {10.1016/j.foodres.2025.117622}, pmid = {41185359}, issn = {1873-7145}, mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; }, abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.}, } @article {pmid41185305, year = {2025}, author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T}, title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117551}, doi = {10.1016/j.foodres.2025.117551}, pmid = {41185305}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; }, abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.}, } @article {pmid41185061, year = {2025}, author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , }, title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {225}, pmid = {41185061}, issn = {2049-2618}, support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; }, mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation & purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; }, abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.

METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.

RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.

CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.}, } @article {pmid41182689, year = {2025}, author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ}, title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {21}, pages = {e71207}, pmid = {41182689}, issn = {1530-6860}, mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; }, abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.}, } @article {pmid41128412, year = {2025}, author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H}, title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.}, journal = {ACS nano}, volume = {19}, number = {43}, pages = {37758-37782}, doi = {10.1021/acsnano.5c10625}, pmid = {41128412}, issn = {1936-086X}, mesh = {Animals ; *Manganese/chemistry/administration & dosage/pharmacology ; *Sepsis/complications/drug therapy/metabolism ; Mice ; *Carbon/chemistry/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Lung Injury/drug therapy/etiology/metabolism/pathology ; Administration, Oral ; Male ; *Quantum Dots/chemistry/administration & dosage ; Lung/drug effects/metabolism ; }, abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.}, } @article {pmid41020558, year = {2025}, author = {Diallo, D and Sene, O and Ngom, D and Khoulé, A and Faye, ET and Dieng, I and Ndione, MHD and Faye, O and Simon-Lorière, E and Diagne, MM and Diallo, M and Sakuntabhai, A and Fall, G}, title = {Detection and genetic characterization of arboviruses and other viruses from mosquitoes collected in southeastern and central Senegal, October 2022.}, journal = {Medical and veterinary entomology}, volume = {39}, number = {4}, pages = {863-874}, doi = {10.1111/mve.70017}, pmid = {41020558}, issn = {1365-2915}, support = {U01AI151758//National Institute of Allergy and Infectious Diseases, National Institues of Health/ ; }, mesh = {Animals ; Senegal ; *Arboviruses/isolation & purification/genetics ; *Culicidae/virology ; Phylogeny ; *Mosquito Vectors/virology ; *Virome ; }, abstract = {The knowledge of the distribution of viruses and their associated mosquito species is still incomplete in Senegal. Additionally, data on the genetic characterization of these viruses are limited. The aim was to update knowledge on the diversity, distribution and genetic relationships of mosquito-associated viruses in Senegal through entomological and molecular surveillance. Mosquitoes were collected in October 2022 across 10 districts in Senegal. Samples were identified morphologically and processed for virome characterization using qRT-PCR and next-generation sequencing. The most common species were Culex cinereus Theobald, 1901, Culex quinquefasciatus Say, 1823, Culex neavei Theobald, 1904, and Culex poicilipes Theobald, 1904 (Diptera: Culicidae). The number of mosquitoes collected varied by habitat and district. We detected 42 isolates of 7 viruses, including Bagaza (BAGV), Barkedji, Sindbis (SINV), Usutu (USUV), Dezidougou, Densovirus and Pestivirus A (PESVA), in 6 mosquito species (Mansonia uniformis, Cx. neavei Theobald, 1901, Anopheles coustani, Cx. cinereus Laveran, 1900, Aedes aegypti Linnaeus, 1762 and Aedes vexans Meigen, 1830) (Diptera: Culicidae). The viruses were mainly detected in mosquitoes collected near ponds (92.9%). BAGV and SINV were detected for the first time in southeastern Senegal. This is also the first association of PESVA with mosquitoes in the field. Phylogenetic analyses revealed that PESVA clustered with strains from Asia and Egypt, BAGV with strains from Senegal and Spain, USUV with strains from Senegal and SINV with strains from Spain and Kenya. This study expands the understanding of mosquito-virus associations in Senegal, revealing new geographic distributions and vectors for several viruses, with implications for arbovirus emergence and surveillance strategies.}, } @article {pmid40998209, year = {2025}, author = {Olsen, IA and Eggesbø, M and Trivedi, U and Timmermann, A}, title = {Per- and polyfluoroalkyl substances and the gut microbiota in infants: A scoping review.}, journal = {Environmental research}, volume = {286}, number = {Pt 2}, pages = {122937}, doi = {10.1016/j.envres.2025.122937}, pmid = {40998209}, issn = {1096-0953}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Fluorocarbons/toxicity ; Infant ; *Environmental Pollutants/toxicity ; *Environmental Exposure ; Infant, Newborn ; Female ; }, abstract = {Per-and polyfluoroalkyl substances (PFASs) are persistent environmental chemicals associated with adverse health effects. Emerging evidence suggests PFAS exposure may influence gut microbiota composition, which is a critical determinant of health particularly during infancy. A systematic search was conducted in PubMed to identify epidemiological studies investigating PFAS exposure and infant gut microbiota. Seven studies met the inclusion criteria, examining a range of PFASs derived from either breast milk, maternal blood, or umbilical cord blood and including from 30 to 789 subjects. These studies used either 16S rRNA sequencing or shotgun metagenomics to assess microbiota changes. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the most frequently examined PFASs. Across studies, exposure to PFASs was associated with both increased and decreased α-diversity. β-diversity shifts were also observed in some studies, suggesting altered microbial structures. PFAS exposure was associated with changes in the abundance of specific taxa, such as increased Enterococcus and decreased Faecalibacterium and Phocaeicola vulgatus. Functional pathway alterations were also reported, including disrupted bile acid metabolism. Variation in study design, covariate adjustment, and methodological approaches likely contribute to the inconsistencies in the observed associations between PFAS exposure and the infant gut microbiota. In conclusion, current evidence suggests that PFAS exposure may influence infant gut microbiota, but more and larger longitudinal studies are needed to better understand whether PFAS exposure is associated with altered gut microbiota composition in infants. This review synthesizes existing evidence on associations between PFAS exposure and gut microbiota composition in infants.}, } @article {pmid40953724, year = {2025}, author = {Lan, T and Zhang, Y and Xie, R and Wu, Q and Wang, H and Du, J and Guo, W}, title = {Aromatic hydrocarbon exposure alters soil microbial communities and redox-driven carbon metabolism.}, journal = {Environmental research}, volume = {286}, number = {Pt 2}, pages = {122845}, doi = {10.1016/j.envres.2025.122845}, pmid = {40953724}, issn = {1096-0953}, mesh = {*Soil Microbiology ; Oxidation-Reduction ; *Soil Pollutants/toxicity ; *Carbon/metabolism ; *Microbiota/drug effects ; *Hydrocarbons, Aromatic/toxicity ; Bacteria/drug effects ; Benzene Derivatives/toxicity ; }, abstract = {The environmental behavior and toxicological impacts of benzene, toluene, ethylbenzene, and xylene (BTEX) have been widely studied. Yet their concentration-dependent effects on soil microbial structure, redox dynamics, and metabolism remain insufficiently understood, constraining predictions of ecosystem responses and the development of targeted bioremediation strategies. Here, we explored how exposure to different concentrations of BTEX reshaped microbial community structure and metabolic function by integrating phased amplicon sequencing, metagenomic analysis, and metabolite profiling. BTEX exposure did not significantly alter the overall microbial richness or diversity across treatment groups but substantially changed the taxonomic composition (Stress = 0.096, R = 0.2284, P = 0.0500). It reduced the dominance of Bacillus and enriched various Clostridium spp. closely associated with acetate and butyrate production. At higher BTEX concentrations, Sporolactobacillus was selectively enriched, directing carbon flow toward lactate production. Functionally, BTEX inhibited early reactions in the pentose phosphate pathway (PPP), while increasing the abundance of genes involved in downstream glycolysis and PPP, leading to rapid pyruvate and NADH accumulation. Meanwhile, inhibition of NADH: ubiquinone oxidoreductase indicated a reduced capacity for respiratory NADH turnover. At slight BTEX concentrations, the redox imbalance increased NADH availability, thereby enhancing alcohol synthesis by 38.03 % (±29.18 %) (P < 0.05). Conversely, high BTEX concentrations enhanced lactate biosynthesis, redirecting carbon and reducing equivalents away from alcohol and acid accumulation (P < 0.05). These findings demonstrate that BTEX reshapes microbial redox dynamics and carbon allocation in a concentration-specific manner, providing mechanistic insights into soil microbiome responses to aromatic hydrocarbon pollution and a basis for designing and optimizing future bioremediation strategies.}, } @article {pmid40940422, year = {2025}, author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL}, title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.}, journal = {The EMBO journal}, volume = {44}, number = {21}, pages = {6226-6252}, pmid = {40940422}, issn = {1460-2075}, support = {R35 GM136390/GM/NIGMS NIH HHS/United States ; R35GM136390//HHS | National Institutes of Health (NIH)/ ; P30GM140963//HHS | National Institutes of Health (NIH)/ ; DBI-1828765//National Science Foundation (NSF)/ ; }, mesh = {*Heme/metabolism ; *Iron/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Bacteroides thetaiotaomicron/metabolism/enzymology/genetics ; Humans ; *Gastrointestinal Microbiome ; Cryoelectron Microscopy ; Models, Molecular ; Protoporphyrins/metabolism ; *Lyases/metabolism/genetics/chemistry ; }, abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.}, } @article {pmid40925458, year = {2025}, author = {Zhao, Z and Gao, B and Henawy, AR and Ur Rehman, K and Ho, JW and Xue, Y and Wu, J and Jiménez, N and Subirats, J and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M}, title = {Effects of chicken manure-derived black soldier fly organic fertilizer on soil carbon and nitrogen cycling: insights from metagenomic and microbial network analysis.}, journal = {Environmental research}, volume = {286}, number = {Pt 2}, pages = {122775}, doi = {10.1016/j.envres.2025.122775}, pmid = {40925458}, issn = {1096-0953}, mesh = {*Fertilizers/analysis ; *Manure/analysis ; Animals ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen Cycle ; Chickens ; Metagenomics ; Carbon ; *Diptera ; Nitrogen ; Microbiota ; }, abstract = {Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis. Compared to the control, BSF organic fertilizer significantly increased soil organic matter by 16.1 % (p < 0.05) and total potassium by 11.0 % (p < 0.05). Metagenomic sequencing revealed that BSF organic fertilizer significantly enhanced soil C and N cycling. For instance, the abundance of carbon fixation genes such as Calvin-Benson-Bassham (CBB) cycle genes pyc, pycA, and pycB increased by 35.7 % (p < 0.01), 107.1 % (p < 0.001), and 14.6 % (p < 0.05), respectively. In nitrogen cycling, denitrification genes nirB, nirK, and nirS increased by 181.5 % (p < 0.001), 102.7 % (p < 0.001), and 25.9 % (p < 0.05), respectively. Furthermore, soils amended with BSF organic fertilizer displayed a 9.9 % higher proportion of positive microbial interactions, particularly enhancing synergistic associations between bacteria and fungi, suggesting improved microbial community stability. Importantly, bacteria and fungi were interdependent in regulating C and N cycling processes, together orchestrating soil ecosystem functions. Overall, BSF organic fertilizers effectively promoted soil C and N cycling and maintained the stability of microbial communities. These findings provide valuable insights for the rational selection of fertilizers and the optimization of fertilization management practices, thereby contributing to the sustainable development of agricultural production.}, } @article {pmid40312036, year = {2025}, author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C}, title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.}, journal = {Beneficial microbes}, volume = {16}, number = {6}, pages = {631-645}, doi = {10.1163/18762891-bja00075}, pmid = {40312036}, issn = {1876-2891}, mesh = {Humans ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant ; *Breast Feeding ; Milk, Human/microbiology ; Feces/microbiology ; Female ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Time Factors ; Infant Formula ; Male ; *Feeding Behavior ; }, abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.}, } @article {pmid41181328, year = {2025}, author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS}, title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1660939}, pmid = {41181328}, issn = {2235-2988}, mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation & purification ; Haemophilus influenzae/isolation & purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Infant ; }, abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.

METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.

RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.

DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.}, } @article {pmid41181319, year = {2025}, author = {Wang, Z and Song, L and Li, D and Jin, Y}, title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1693796}, pmid = {41181319}, issn = {2235-2988}, mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; }, abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.}, } @article {pmid41177609, year = {2026}, author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W}, title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.}, journal = {Journal of environmental sciences (China)}, volume = {160}, number = {}, pages = {300-307}, doi = {10.1016/j.jes.2025.04.024}, pmid = {41177609}, issn = {1001-0742}, mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; }, abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.}, } @article {pmid41005405, year = {2025}, author = {Gomes, BM and de Oliveira, GS and de Melo, VS and Rossini, NO and Adriani, PP and Dias, MVB and Chambergo, FS}, title = {Structural and functional characterization of a bifunctional GH43 α-L-arabinofuranosidase/β-xylosidase from the metagenome of Pseudacanthotermes militaris gut.}, journal = {International journal of biological macromolecules}, volume = {329}, number = {Pt 2}, pages = {147909}, doi = {10.1016/j.ijbiomac.2025.147909}, pmid = {41005405}, issn = {1879-0003}, mesh = {*Glycoside Hydrolases/chemistry/metabolism/genetics ; *Xylosidases/chemistry/metabolism/genetics ; Substrate Specificity ; *Metagenome ; Animals ; *Isoptera/enzymology/genetics/microbiology ; Kinetics ; *Gastrointestinal Microbiome ; Models, Molecular ; Catalytic Domain ; Amino Acid Sequence ; }, abstract = {The pursuit of sustainable energy has intensified the search for efficient biocatalysts to convert lignocellulosic biomass. In this context, we characterized a novel bifunctional enzyme, TerARA, identified from the gut metagenome of the termite Pseudacanthotermes militaris. Belonging to the glycoside hydrolase 43 (GH43) family, TerARA was heterologously expressed in E. coli BL21 and purified. The enzyme demonstrated bifunctional activity toward synthetic substrates p-nitrophenyl-α-L-arabinofuranoside (pNP-Araf) (387.22 ± 74.2 U/mg) and p-nitrophenyl-β-D-xylopyranoside (pNP-Xyl) (330.82 ± 31.2 U/mg), with higher catalytic efficiency for pNP-Araf (9.14 s[-1]·mM[-1]), suggesting functional preference as an α-L-arabinofuranosidase. Activity modulation by metal ions revealed that Ca[2+] slightly improved efficiency toward pNP-Araf (to 9.58 s[-1]·mM[-1] at 1 mM), while Zn[2+] reduced efficiency for pNP-Xyl except at 5 mM (6.65 s[-1]·mM[-1]). Zn[2+] also enhanced enzymatic stability, maintaining 80 % activity in pNP-Xyl hydrolysis. Crystallographic analysis at 2.0 Å resolution revealed a 43 Glycosyl Hydrolase catalytic domain with a five-bladed β-propeller fold and two Ca[2+] ions and a Carbohydrate-Binding Module (CBM) domain with a β-sandwich fold likely involved in substrate interaction. Conserved catalytic residues, binding sites, and Ca[2+] stabilizing effects were identified. TerARA's bifunctionality and structural features support its application in hemicellulose degradation and biomass conversion.}, } @article {pmid40722249, year = {2025}, author = {Hilberath, J and Busch, A and Schoppmeier, U and Schmauder, K and Oberhettinger, P and Marschal, M and Slavetinsky, C and Sturm, E and Peter, S and D'Alvise, P}, title = {Small intestinal bacterial overgrowth and dysbiosis in children with intestinal failure: A descriptive cohort study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {49}, number = {8}, pages = {964-974}, doi = {10.1002/jpen.2808}, pmid = {40722249}, issn = {1941-2444}, mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Intestine, Small/microbiology ; Child, Preschool ; Child ; *Gastrointestinal Microbiome ; Infant ; Prospective Studies ; Cohort Studies ; *Intestinal Failure/microbiology/complications ; Bacteria/growth & development ; Short Bowel Syndrome/microbiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is a clinical and diagnostic challenge in pediatric intestinal failure. This study aimed to assess SIBO and dysbiosis in children with intestinal failure and to analyze clinical characteristics as well as cultural and metagenomic sequencing results from different sampling methods.

METHODS: Descriptive, single-center cohort study in intestinal failure patients with prospective collection of intraluminal aspirate, epithelial brush swab, mucosal biopsy, and small bowel stoma stool for SIBO diagnosis, defined as ≥10[3] CFU/ml of enteric, colonic-type bacteria, and microbiome analysis via whole-genome sequencing. Statistical testing included receiver operating characteristic analysis, chi-square test, and independent samples t test.

RESULTS: Forty-four children with intestinal failure were analyzed (median age 58 months; female 48%; short bowel syndrome 70%). Sixty-six percent of samples were positive for SIBO. In 93%, all three endoscopic sampling methods showed congruent results. SIBO-positive cases were associated (P < 0.05) with small bowel dilatation, proton pump inhibitor use, intestinal inflammation, elevated direct bilirubin and hepatocellular enzyme levels, and a history of liver fibrosis and central venous catheter infections. Metagenomic sequencing revealed microbial dysbiosis in intestinal failure patients, with SIBO-positive cases showing higher microbial reads, lower alpha diversity, and increased abundance of Enterobacteriaceae and enteric anaerobes.

CONCLUSION: SIBO and dysbiosis are common in children with intestinal failure and associated with liver injury, central line-associated bloodstream infections, and intestinal inflammation. Cultural diagnosis of SIBO using mucosal biopsies or brush swabs are alternatives to small bowel aspirates. Metagenomic sequencing is feasible, and high microbial read numbers are indicative of SIBO.}, } @article {pmid41175763, year = {2025}, author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X}, title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140321}, doi = {10.1016/j.jhazmat.2025.140321}, pmid = {41175763}, issn = {1873-3336}, abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.}, } @article {pmid39756573, year = {2025}, author = {Shen, H and Li, Y and Pi, Q and Tian, J and Xu, X and Huang, Z and Huang, J and Pian, C and Mao, S}, title = {Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate.}, journal = {Journal of advanced research}, volume = {77}, number = {}, pages = {821-835}, doi = {10.1016/j.jare.2025.01.005}, pmid = {39756573}, issn = {2090-1224}, mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/drug effects ; *Deep Learning ; *Antimicrobial Peptides/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; Molecular Dynamics Simulation ; *Ruminants/microbiology ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Staphylococcal Infections/drug therapy/microbiology ; Computational Biology/methods ; }, abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery.

OBJECTIVES: The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity.

METHODS: We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate.

RESULTS: The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death.

CONCLUSION: This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.}, } @article {pmid41175161, year = {2025}, author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV}, title = {Gellan gum-based media recover more diverse microbial communities from soil material.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {338}, pmid = {41175161}, issn = {1432-072X}, support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation & purification/classification/genetics/growth & development ; *Microbiota ; }, abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.}, } @article {pmid41174950, year = {2025}, author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, MÀ and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G}, title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {12}, pages = {e70418}, pmid = {41174950}, issn = {1478-3231}, support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; }, mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; }, abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.}, } @article {pmid41174518, year = {2025}, author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B}, title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {704}, pmid = {41174518}, issn = {1471-2180}, mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; }, abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.

RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.

CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.}, } @article {pmid41174459, year = {2025}, author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C}, title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 2}, pages = {117386}, doi = {10.1016/j.foodres.2025.117386}, pmid = {41174459}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.}, } @article {pmid41174397, year = {2025}, author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C}, title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 2}, pages = {117319}, doi = {10.1016/j.foodres.2025.117319}, pmid = {41174397}, issn = {1873-7145}, mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; }, abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.}, } @article {pmid41173910, year = {2025}, author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW}, title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9658}, pmid = {41173910}, issn = {2041-1723}, support = {R01NS055349//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32GM148382//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Dysbiosis/microbiology/mortality/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; *Malaria/mortality/microbiology/complications ; Female ; Male ; Infant ; Feces/microbiology ; Child ; Escherichia coli/isolation & purification/genetics ; Metagenome ; Enterobacteriaceae/isolation & purification/genetics ; Patient Discharge ; }, abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.}, } @article {pmid41173905, year = {2025}, author = {Adhikary, R and Alkhatib, AEA and Hazra, S}, title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38127}, pmid = {41173905}, issn = {2045-2322}, mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; }, abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.}, } @article {pmid41173568, year = {2025}, author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I}, title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.}, journal = {Endocrinologia, diabetes y nutricion}, volume = {72}, number = {9}, pages = {501624}, doi = {10.1016/j.endien.2025.501624}, pmid = {41173568}, issn = {2530-0180}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; }, abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.}, } @article {pmid41172529, year = {2025}, author = {Lima, JD and Rivadavea, WR and Calgaro, LC and Alberton, O and Costa, MSSM and Lima, JC and Monteiro, PHR and Kuhn, EV and Silva, GJ}, title = {Biological dynamics of no-tillage soils in the western region of Paraná.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {85}, number = {}, pages = {e298630}, doi = {10.1590/1519-6984.298630}, pmid = {41172529}, issn = {1678-4375}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Brazil ; Nitrogen/analysis ; *Agriculture/methods ; Biomass ; Biodiversity ; Fungi/classification ; Carbon/analysis ; }, abstract = {This study investigates soil dynamics on farms in the western region of Paraná, Brazil, highlighting the importance of biological parameters in agriculture. In particular, focusing on the interaction of management practices with soil biodiversity and biological functions, the aim is to understand and promote sustainable and efficient agricultural practices. To do this, we collected soil samples from 15 farms close to Toledo, Paraná, Brazil. These samples were then analyzed to determine biological and physicochemical parameters using techniques such as carbon and nitrogen microbial biomass, metabolic coefficient, basal respiration, bacterial and fungal biomass, and length of the hyphae. The most contrasting soils were evaluated for physicochemical composition and metagenomic analyses. The results showed significant differences in biological parameters between 2020 and 2021, including fungal biomass, hyphae length, and soil basal respiration. Statistical analyzes revealed strong relationships between biological variables, notably the correlation between fungal hyphae and total nitrogen. Climate changes and management practices appear to influence the microbial composition and biological functions of the soil over the years. Soil P9 stood out with superior biological activity and richer microbial diversity, contrasting with soil P13. These differences reflect the influence of management and climatic conditions on soil composition and biological functions. The microbial comparison of the soils emphasized the need for continuous and careful agricultural management, highlighting the importance of biodiversity and ecological functionality of the soil for agricultural sustainability. So, the study underscores the relevance of considering soil biological parameters, in addition to physicochemical aspects, to optimize soil health and productivity.}, } @article {pmid41171541, year = {2025}, author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C}, title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {35}, pmid = {41171541}, issn = {1573-4978}, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; }, abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.}, } @article {pmid41168432, year = {2025}, author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, Â and Castrillo, G and Wagner, MR}, title = {Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2823-2844}, pmid = {41168432}, issn = {2058-5276}, support = {IOS-2016351//National Science Foundation (NSF)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Droughts ; *Soil Microbiology ; *Microbiota/genetics ; Zea mays/physiology/genetics/microbiology ; Soil/chemistry ; *Rain ; Kansas ; Plant Roots/microbiology/genetics ; Stress, Physiological ; Metagenome ; Adaptation, Physiological ; Water/metabolism ; *Plants/microbiology/genetics ; Bacteria/classification/genetics ; }, abstract = {Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.}, } @article {pmid41168431, year = {2025}, author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ}, title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2720-2735}, pmid = {41168431}, issn = {2058-5276}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; DK120485//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Uganda ; Alkynes ; Metagenomics ; Benzoxazines/therapeutic use/adverse effects ; Male ; Female ; Feces/microbiology ; Cyclopropanes ; Adult ; Botswana ; *Anti-Retroviral Agents/therapeutic use ; Middle Aged ; United States ; Reverse Transcriptase Inhibitors/therapeutic use ; *Anti-HIV Agents/therapeutic use ; Bacteria/classification/genetics/drug effects/isolation & purification ; }, abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.}, } @article {pmid41131367, year = {2025}, author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C}, title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2686-2701}, pmid = {41131367}, issn = {2058-5276}, support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; }, mesh = {*Hydrogenase/metabolism/genetics ; Humans ; Hydrogen/metabolism ; *Gastrointestinal Microbiome ; Fermentation ; *Bacteria/genetics/enzymology/classification/growth & development/metabolism/isolation & purification ; Metagenomics ; Feces/microbiology ; Bacteroidetes/growth & development/metabolism/genetics ; Firmicutes/growth & development/genetics/metabolism/enzymology ; Crohn Disease/microbiology ; *Gastrointestinal Tract/microbiology ; Iron-Sulfur Proteins/metabolism/genetics ; Healthy Volunteers ; }, abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.}, } @article {pmid41073663, year = {2025}, author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF}, title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2797-2807}, pmid = {41073663}, issn = {2058-5276}, support = {K01-DK102771//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Mice ; *Bacteroides fragilis/genetics/metabolism/immunology ; *Glycolipids/immunology/chemistry/metabolism/biosynthesis ; Natural Killer T-Cells/immunology ; Galactosyltransferases/metabolism/genetics ; Symbiosis ; Mice, Inbred C57BL ; Colon/immunology/microbiology ; Infant ; Galactosylceramides/metabolism/biosynthesis ; Female ; *Bacteria/metabolism/classification/genetics ; Lymphocyte Activation ; }, abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.}, } @article {pmid40972730, year = {2026}, author = {Wang, X and Chen, M and Su, Y and Zhang, X and Chen, J and Huang, Z and Xie, J and Xie, Q and He, L and Su, L and Su, Z and Wang, H and Li, Y}, title = {A novel cholesterol-reducing mechanism of polygonati rhizoma: Dual action via Bacteroides-mediated cholesterol sulfonation and feedback inhibition of ACAT2 by sulfated metabolite.}, journal = {Journal of ethnopharmacology}, volume = {355}, number = {Pt A}, pages = {120619}, doi = {10.1016/j.jep.2025.120619}, pmid = {40972730}, issn = {1872-7573}, mesh = {Animals ; Mice ; Male ; *Cholesterol/metabolism/blood ; *Polygonatum/chemistry ; *Hypercholesterolemia/drug therapy ; Gastrointestinal Microbiome/drug effects ; Molecular Docking Simulation ; *Bacteroides/metabolism/drug effects ; *Anticholesteremic Agents/pharmacology/isolation & purification ; *Phosphatidylcholine-Sterol O-Acyltransferase/antagonists & inhibitors/metabolism ; Rhizome ; Disease Models, Animal ; *Plant Extracts/pharmacology ; Animals, Outbred Strains ; }, abstract = {Polygonati Rhizoma (PR) has the function of "invigorating spleen and tonifying kidney", and is historically applied as a homology of medicine and food to prevent and treat dyslipidemia in China. However, there is limited experimental evidence to support this application, and the underlying mechanism has not been fully deciphered.

AIM OF THE STUDY: To analyze the composition and illuminate the cholesterol-lowering potential and molecular mechanism of PR's aqueous extract (PRE) in high-fat emulsion (HFE)-induced hypercholesterolemia mouse model.

MATERIALS AND METHODS: Ion chromatograph was employed to determine the monosaccharide composition of PRE. HFE-induced Kunming mouse model was constructed to evaluate the anti-hypercholesterolemia effect of PRE. Metagenomic sequences and liquid chromatography-mass spectrometry (LC-MS) analysis were performed to elucidate the mechanism through which PR regulated cholesterol metabolism. Antibiotic cocktail (ABX) intervention and fecal microbiota transplantation (FMT) were used to validate whether PRE regulated cholesterol metabolism through the intestinal microbiota. The cholesterol-reducing effect of cholesterol sulfate (CS) was explored in poloxamer 407 (P407)-induced mouse model of dyslipidemia. Molecular docking and molecular dynamics (MD) simulation were also employed to elucidate the underlying mechanisms. Furthermore, a combination of qRT-PCR, Western blot, and surface plasmon resonance (SPR) were employed to delineate its mechanism.

RESULTS: Our study indicated that the polysaccharides of PRE were mainly composed of fructose (92.33 %) and glucose (5.25 %). PRE treatment effectively blocked body weight gain, significantly decreased serum and hepatic levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C), and increased high-density lipoprotein cholesterol (HDL-C) level. Additionally, PRE ameliorated hepatic lipid accumulation in mice with HFE-elicited hypercholesterolemia. Notably, metagenomic sequencing and LC-MS analysis indicated that PRE markedly increased the abundance of intestinal genera Bacteroides and significantly elevated the fecal CS concentration in HFE mice. Genome-based functional analysis further indicated that cofactors of sulfonation (ATP sulfurylase CysD and CysN, BT0414-BT0415) were significantly upregulated after treatment with PRE. The cholesterol-lowering effect of PRE was largely contingent upon microbial conversion of cholesterol-to-CS mediated by Bacteroides, as validated by antibiotics-induced intestinal microbiota depletion in pseudo-germ-free model and restoration of gut microbiota through FMT. In vitro study also showed that PRE promoted the growth of Bacteroides thetaiotaomicron. Furthermore, CS markedly alleviated serum, hepatic, bile, and fecal levels of TG, TC, LDL-C, HDL-C, and TBA, indicative of appreciable lipid-lowering effect. MD simulation and SPR results indicated that CS directly bound to ACAT2. Consistent with this interaction, CS greatly downregulated the mRNA and protein expression of ACAT2 in small intestinal tissue.

CONCLUSION: These findings for the first time suggested that PR acted as a prebiotic agent to ameliorate hypercholesterolemia, at least in part, via dual mechanism involving modulation of Bacteroides-mediated sulfonation metabolic pathway and feedback inhibition of ACAT2 by CS, highlighting its therapeutic potential for cholesterol-related disorders. This work might also offer novel mechanistic insight and further buttressed the ethnopharmacological application of PR in the therapy of hypercholesterolemia.}, } @article {pmid40812707, year = {2025}, author = {Wu, J and Chen, Y and Zhao, J and O'Brien, JW and Coin, L and Hai, FI and Sanderson-Smith, M and Jiang, G}, title = {Impact of human lifestyle on the pathogenic potential of urban wastewater.}, journal = {Environmental research}, volume = {286}, number = {Pt 1}, pages = {122591}, doi = {10.1016/j.envres.2025.122591}, pmid = {40812707}, issn = {1096-0953}, mesh = {*Wastewater/microbiology ; Humans ; *Life Style ; Australia ; Virulence Factors/genetics ; *Bacteria/pathogenicity/genetics ; Cities ; *Microbiota ; }, abstract = {Domestic wastewater has been known for its pathogenic potential including the presence of pathogenic bacteria, virulence factor genes (VFGs) and antibiotic resistance genes (ARGs). While previous studies have investigated regional differences in microbial communities, the influence of population lifestyle factors on the pathogenic potential of wastewater microbiomes remains poorly understood. In this study, we analyzed ten Australian wastewater treatment plants (WWTPs) using Nanopore metagenomic sequencing to profile pathogens, ARGs, and VFGs, and examined their associations with health-related behaviors such as smoking, alcohol consumption, and obesity. A total of 196 pathogenic species, 951 ARG subtypes, and 380 VFGs were detected. Staphylococcus aureus was the most abundant pathogen, macB the dominant ARG, and lipooligosaccharides (LOS) the most prevalent VFG. While pathogen and ARG profiles were relatively stable across sites and showed limited association with lifestyle variables, VFG profiles demonstrated significant correlations with smoking rates, alcohol consumption, and nicotine levels in wastewater. Co-occurrence network analysis revealed strong interconnectivity among VFGs and between VFGs and ARGs, suggesting potential co-selection. Principal component analysis and diversity metrics further confirmed distinct patterns in VFG distribution across sites. These findings suggest VFGs as potentially sensitive indicators of behavioral health risks in wastewater-based epidemiology.}, } @article {pmid41171126, year = {2025}, author = {She, J and Qian, PY and Wu, L}, title = {DOO: integrated multi-omics resources for deep ocean organisms.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1096}, pmid = {41171126}, issn = {1362-4962}, support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; }, abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.}, } @article {pmid41171124, year = {2025}, author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S}, title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf1098}, pmid = {41171124}, issn = {1362-4962}, support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; }, abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.}, } @article {pmid41168883, year = {2025}, author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M}, title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {224}, pmid = {41168883}, issn = {2049-2618}, support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; }, mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth & development/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.

RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (> 23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2 days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15 days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.

CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.}, } @article {pmid41168882, year = {2025}, author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC}, title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {222}, pmid = {41168882}, issn = {2049-2618}, support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; }, abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.}, } @article {pmid41168702, year = {2025}, author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML}, title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.}, journal = {Genetics, selection, evolution : GSE}, volume = {57}, number = {1}, pages = {64}, pmid = {41168702}, issn = {1297-9686}, support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.

RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.

CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.}, } @article {pmid41168291, year = {2025}, author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM}, title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37987}, pmid = {41168291}, issn = {2045-2322}, mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; }, abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.}, } @article {pmid41165913, year = {2025}, author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM}, title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {11}, pages = {1268}, pmid = {41165913}, issn = {1573-2959}, mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; }, abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.}, } @article {pmid41066239, year = {2025}, author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE}, title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.}, journal = {Cell reports}, volume = {44}, number = {10}, pages = {116413}, doi = {10.1016/j.celrep.2025.116413}, pmid = {41066239}, issn = {2211-1247}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/virology/pathology ; *Bacteriophages/genetics/physiology ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Sputum/microbiology/virology ; Lung/microbiology/virology ; Severity of Illness Index ; }, abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.}, } @article {pmid40966087, year = {2025}, author = {Pu, Y and Qi, X and Huang, L and Wu, W and Zhou, X and Li, W and Yang, Z and Kong, M and Shen, J and Qi, W and Sun, Z and Mei, Z and Wang, Q and Yang, W and Gao, X and Wang, X and Liu, Z and Yuan, C and Zheng, Y}, title = {Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.}, journal = {Cell reports}, volume = {44}, number = {10}, pages = {116297}, doi = {10.1016/j.celrep.2025.116297}, pmid = {40966087}, issn = {2211-1247}, mesh = {Humans ; Aged ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; *Metabolome ; Male ; Middle Aged ; Aged, 80 and over ; *Metagenome ; *Sleep/physiology ; *Frailty/blood/microbiology/metabolism ; *Pyruvic Acid/metabolism ; }, abstract = {Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.}, } @article {pmid41164885, year = {2025}, author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T}, title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {10}, pages = {e70844}, doi = {10.1002/alz.70844}, pmid = {41164885}, issn = {1552-5279}, support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Genève/ ; //Fondation Segré, Genève/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Genève/ ; //Fondation Edmond J. Safra, Genève/ ; //Fondation Minkoff, Genève/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et René Keller, Genève/ ; //Fondation AETAS, Genève/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //Hôpitaux Universitaires de Genève/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; }, abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.

METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.

RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from < 2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.

DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.

HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.}, } @article {pmid41163852, year = {2025}, author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H}, title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1660970}, pmid = {41163852}, issn = {2235-2988}, mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation & purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; }, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.

METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.

RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.

DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.}, } @article {pmid41163226, year = {2025}, author = {Huang, S and Chen, Y and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W}, title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {350}, pmid = {41163226}, issn = {1743-422X}, support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; }, mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.

RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n = 1), Paramyxoviridae (n = 1), Polyomaviridae (n = 1), Parvoviridae (n = 7), Circoviridae (n = 6), and Genomoviridae (n = 1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.

CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.}, } @article {pmid41163171, year = {2025}, author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z}, title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {24}, number = {1}, pages = {59}, pmid = {41163171}, issn = {1476-0711}, support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&D Program of the China Ministry of Science and Technology/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.

METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.

RESULTS: No significant differences were observed in age (62.22 ± 5.74 vs. 58.23 ± 7.55, p = 0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p = 0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p < 0.05) and distinct beta diversity clustering (p < 0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p < 0.0001). Neutral modeling indicated stochastic assembly (R² >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.

CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.}, } @article {pmid41163130, year = {2025}, author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD}, title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {967}, pmid = {41163130}, issn = {1471-2164}, support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; }, mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; }, abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.

RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.

CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.}, } @article {pmid41162595, year = {2025}, author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L}, title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37813}, pmid = {41162595}, issn = {2045-2322}, support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation & purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; }, abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.}, } @article {pmid41162178, year = {2025}, author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H}, title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2506012}, doi = {10.4014/jmb.2506.06012}, pmid = {41162178}, issn = {1738-8872}, mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; DNA, Bacterial/genetics ; }, abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.}, } @article {pmid41086517, year = {2026}, author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q}, title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.}, journal = {Virology}, volume = {613}, number = {}, pages = {110712}, doi = {10.1016/j.virol.2025.110712}, pmid = {41086517}, issn = {1096-0341}, mesh = {*Extracellular Vesicles/virology/metabolism ; *Phosphatidylserines/metabolism ; Humans ; Feces/virology ; Metagenomics ; Gastrointestinal Microbiome ; Virome ; *Viruses/genetics/classification/isolation & purification/metabolism ; }, abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.}, } @article {pmid41062001, year = {2025}, author = {Ghaffar, T and Valeriani, F and Romano Spica, V}, title = {The sex related differences in health and Disease: A systematic review of sex-specific gut microbiota and Possible implications for microbial pathogenesis.}, journal = {Microbial pathogenesis}, volume = {209}, number = {}, pages = {108094}, doi = {10.1016/j.micpath.2025.108094}, pmid = {41062001}, issn = {1096-1208}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Female ; Male ; Sex Factors ; Mice ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Sex Characteristics ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.

METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.

RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.

CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.}, } @article {pmid41033626, year = {2025}, author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H}, title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.}, journal = {Environmental research}, volume = {286}, number = {Pt 3}, pages = {122985}, doi = {10.1016/j.envres.2025.122985}, pmid = {41033626}, issn = {1096-0953}, mesh = {*Rhizosphere ; *Cadmium/metabolism ; *Microbiota/drug effects ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Iron/metabolism ; Manganese/metabolism ; Oryza/microbiology ; Sulfur/metabolism ; Bacteria ; Environmental Restoration and Remediation/methods ; }, abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems (1) iron/manganese oxidation (e.g., feoB): associated with iron-manganese plaque (IP) formation (2) sulfate reduction (e.g., dsrA); linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.}, } @article {pmid41015172, year = {2025}, author = {Luo, S and Yuan, J and Song, Y and Qi, J and Zhu, M and Feng, H and Zhao, Y and Mei, W and Fu, F and Li, X and Song, C}, title = {Bacterial network complexity drives carbon, nitrogen and phosphorus metabolism potential under short-term soil water content changes in wetlands.}, journal = {Environmental research}, volume = {286}, number = {Pt 3}, pages = {122952}, doi = {10.1016/j.envres.2025.122952}, pmid = {41015172}, issn = {1096-0953}, mesh = {*Wetlands ; *Phosphorus/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Carbon/metabolism ; Soil/chemistry ; China ; *Bacteria/metabolism ; Water/analysis ; Droughts ; Microbiota ; }, abstract = {Wetland soil microbial communities play pivotal roles in biogeochemical cycling; however, how their network complexity mediates carbon (C), nitrogen (N), and phosphorus (P) metabolism in response to soil water content (SWC) changes remains unclear. In this study, soil samples from the Zhalong, Momoge and Xianghai wetlands in Songnen Plain of China were incubated under natural (CK), drought (10 % SWC), and high SWC (50 % SWC) conditions, followed by metagenomic sequencing to evaluate the impact of SWC changes on bacterial community structure and function. The results showed that soil bacterial diversity and network complexity decreased under drought but recovered under high SWC, with Proteobacteria and Actinobacteria displaying divergent responses. C fixation pathways (rTCA and DC-HB cycles) were significantly enriched under 50 % SWC, which correlated strongly with enhanced bacterial interactions. The abundance of denitrification genes (norBC, nosZ) decreased under drought but increased under high SWC. P metabolism (purine metabolism and two-component systems) showed strong SWC dependence, with key genes (PstS, phnDC) increased in abundance under 50 % SWC. Notably, bacterial network complexity tightly coupled with metabolic pathways, indicating SWC driven community restructuring regulates wetland soil C, N and P cycling. These findings underscore the critical importance of hydrological management in maintaining bacterial-mediated nutrient cycling functions of wetland ecosystem under climate change.}, } @article {pmid41162143, year = {2025}, author = {Hutchings, P and Rowe, CE and Byrne, M and Przeslawski, R}, title = {Taxonomy is a foundation of marine science, and it is in trouble.}, journal = {Advances in marine biology}, volume = {101}, number = {}, pages = {197-212}, doi = {10.1016/bs.amb.2025.08.003}, pmid = {41162143}, issn = {2162-5875}, mesh = {*Classification/methods ; Animals ; Conservation of Natural Resources ; *Aquatic Organisms/classification ; Biodiversity ; *Marine Biology/education ; Australia ; }, abstract = {This volume of Advances highlights not only the importance of marine benthic diversity in several regions of the world but also the impediments to describing this fauna. Taxonomy is the science of classifying organisms and is the bedrock of marine biodiversity research and conservation, yet it faces significant decline in Australia. Thus, it is critical that the scientific community understand why taxonomy is so important. This paper underscores the foundational role of taxonomy in marine ecology, using case studies that highlight its critical relevance to species management, conservation policy, and international trade regulation. Despite extensive research and funding, unresolved taxonomies continue to affect our management of ecologically and economically important taxa, including crown-of-thorns seastar (Acanthaster spp.), exploited sea cucumbers (Holothuroidea), and invasive Cassiopea jellyfish. These ambiguities hamper accurate species identification, hinder effective conservation strategies, and complicate regulatory listings under frameworks such as CITES and the IUCN Red List. Key challenges include dwindling taxonomic expertise, reduced funding, lack of university training, and limited career pathways, all of which contribute to Australia's inability to adequately explore and manage its vast marine jurisdiction. The paper advocates for immediate systemic reforms through a series of 11 recommendations related to revitalizing taxonomic education, fostering museum-university partnerships, supporting early career researchers, and investing in infrastructure to enable species discovery. Taxonomic rigor is also essential to validate modern tools like eDNA, metagenomics, and image-based analysis. Without it, efforts to safeguard biodiversity and to foster a sustainable blue economy risk failure.}, } @article {pmid41161821, year = {2025}, author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L}, title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {10}, pages = {}, doi = {10.1136/jitc-2025-012444}, pmid = {41161821}, issn = {2051-1426}, mesh = {Humans ; Male ; Female ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; Middle Aged ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Aged ; *Lung/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.

METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.

RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).

CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.}, } @article {pmid41160250, year = {2025}, author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y}, title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.}, journal = {Clinical oral investigations}, volume = {29}, number = {11}, pages = {543}, pmid = {41160250}, issn = {1436-3771}, support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; }, mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; }, abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.

MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.

RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.

CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.

CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.

TRIAL REGISTRATION: ITMCTR2024000616.}, } @article {pmid41160143, year = {2025}, author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM}, title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {183}, pmid = {41160143}, issn = {1572-9699}, mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.}, } @article {pmid41159034, year = {2025}, author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN}, title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1655428}, pmid = {41159034}, issn = {1664-3224}, mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.

METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.

RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.

DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.}, } @article {pmid41157632, year = {2025}, author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K}, title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101362}, pmid = {41157632}, issn = {1999-4915}, support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; }, mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation & purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; }, abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.}, } @article {pmid41157620, year = {2025}, author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ}, title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101349}, pmid = {41157620}, issn = {1999-4915}, support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation & purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; }, abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.}, } @article {pmid41157605, year = {2025}, author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J}, title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101334}, pmid = {41157605}, issn = {1999-4915}, support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; }, mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation & purification ; Genotype ; Genetic Variation ; }, abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.}, } @article {pmid41157584, year = {2025}, author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS}, title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/v17101312}, pmid = {41157584}, issn = {1999-4915}, support = {202271250010//Parliamentary Amendment from the São Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; }, mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; }, abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.}, } @article {pmid41156832, year = {2025}, author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P}, title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.}, journal = {Microorganisms}, volume = {13}, number = {10}, pages = {}, doi = {10.3390/microorganisms13102373}, pmid = {41156832}, issn = {2076-2607}, support = {1671/22-03-2023//Green Fund/ ; }, abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.}, } @article {pmid41156619, year = {2025}, author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB}, title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/pathogens14101008}, pmid = {41156619}, issn = {2076-0817}, mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; }, abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.}, } @article {pmid41156596, year = {2025}, author = {Dao, TK and Pham, TTN and Nguyen, HD and Dam, QT and Phung, TBT and Nguyen, TVH and Nguyen, TQ and Hoang, KC and Do, TH}, title = {Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/pathogens14100985}, pmid = {41156596}, issn = {2076-0817}, support = {ĐTĐLCN.63/22//Ministry of Science and Technology, Vietnam/ ; }, mesh = {Humans ; *Diarrhea/microbiology/virology ; *Dysbiosis/microbiology/virology ; Metagenomics/methods ; Infant ; *Bacteriophages/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Male ; Female ; Vietnam ; Child, Preschool ; *Metagenome ; Bacteria/classification/genetics/virology ; *Virome ; Feces/microbiology/virology ; }, abstract = {Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.}, } @article {pmid41156563, year = {2025}, author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M}, title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {20}, pages = {}, doi = {10.3390/nu17203312}, pmid = {41156563}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; }, abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.}, } @article {pmid41155136, year = {2025}, author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T}, title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.}, journal = {International journal of molecular sciences}, volume = {26}, number = {20}, pages = {}, doi = {10.3390/ijms26209841}, pmid = {41155136}, issn = {1422-0067}, support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; }, mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation & purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; }, abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.}, } @article {pmid41152727, year = {2025}, author = {Chen, L and Wang, C and Zhang, H and Wu, Y and Li, F and Shi, H and Ren, Z and Chen, Y and Huang, J and Zhao, D and Pan, J and Lu, H and Zheng, S}, title = {Characterization of microbiota dysbiosis in papillary thyroid carcinoma and benign thyroid nodules: low abundance of intestinal butyrate-producing bacteria.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {691}, pmid = {41152727}, issn = {1471-2180}, support = {2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//the National Natural Science Foundation of China/ ; JNL-2022001A//the Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; *Thyroid Cancer, Papillary/microbiology ; *Butyrates/metabolism ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Feces/microbiology ; *Thyroid Nodule/microbiology ; Adult ; *Thyroid Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: The thyroid-gut axis refers to the intricate relationships among the gut, intestinal microbiota, and thyroid gland, and it is speculated to play an important role in the development of thyroid diseases. The aim of this study was to identify the differentiated bacteria in the intestinal microbiota associated with papillary thyroid carcinoma (PTC) and benign thyroid nodules (BTNs) to offer potential avenues for further exploration and therapeutic interventions.

METHODS: Faecal microbiotas of 197 subjects (73 from subjects with BTNs, 62 from subjects with PTC, and 62 from sex- and age-matched controls) were characterized by sequencing the V3-V4 region of 16 S rDNA using the Illumina NovaSeq 6000 platform. Microbiomics and machine learning-assisted approaches were used to identify the PTC-/BTN-associated intestinal microbial indicators.

RESULTS: Compared with the abundance of coabundant groups (CAGs) in the PTC, BTN, and control groups, the abundance of two Genus-CAGs consisting of butyrate producers, such as Blautia, Lachnoclostridium, Lachnospiraceae_unclassified, Eisenbergiella, Flavonifractor and Hungatella, was lower in the PTC group than in the control group. In particular, both ANCOM-BC2 and Wilcoxon rank-sum test results consistently demonstrated significant enrichment of the butyrate-producing genera Oscillibacter, Coprobacter, and Colidextribacter in both BTN patients and healthy controls. The majority of discriminatory amplicon sequence variants (ASVs) that could discriminate PTCs from controls, as well as from BTNs, were from Prevotella, Streptococcus, Bacteroides, and butyrate-producing groups, such as the Oscillibacter, Lachnospiraceae, and Christensenellaceae (R7) groups. ASV indicators from Prevotella and Streptococcus were most abundant in the PTC group, and those from Bacteroides and the butyrate-producing/-promoting group were least abundant in the PTC group. Additionally, the ASVs that could discriminate the BTN group from the control group, as well as PTC group included other butyrate-producing groups, the Clostridium_sensu_stricto group, and the Eubacterium_siraeum group.

CONCLUSIONS: This study demonstrates that dysbiosis linked to thyroid nodules is marked by a substantial decline in intestinal butyrate-producing and butyrate-promoting taxa. Future work to confirm these results should include shotgun metagenomic sequencing paired with quantitative analyses of gene abundance and expression to fully ascertain the functional implications.}, } @article {pmid41152726, year = {2025}, author = {Zou, Y and Zou, Q and Wang, Y and Han, C}, title = {Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {693}, pmid = {41152726}, issn = {1471-2180}, support = {62402344//Youth Found of the National Natural Science Foundation of China/ ; 62373080//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Seasons ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; China ; Feces/microbiology ; }, abstract = {BACKGROUND: Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of Eospalax rothschildi, a subterranean zokor endemic to China.

RESULTS: Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of α-galactosidase and β-galactosidase genes from enriched microbial populations, particularly Bacteroides, unclassified_f_Lachnospiraceae, Roseburia, and Faecalibacterium. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in E. rothschildi during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.

CONCLUSIONS: Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of E. rothschildi.}, } @article {pmid41152332, year = {2025}, author = {Ciuchcinski, K and Bluszcz, A and Dziewit, L}, title = {Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1702}, pmid = {41152332}, issn = {2052-4463}, support = {BOB-IDUB-622-105/2024//Uniwersytet Warszawski (University of Warsaw)/ ; }, mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Poland ; Salinity ; *Plasmids ; *Microbiota ; Metagenomics ; }, abstract = {Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.}, } @article {pmid41152000, year = {2025}, author = {Saguti, F and Wang, H and Churqui, MP and Tunovic, T and Holmer, L and Pettersson, Ä and Schleich, C and Pott, BM and Bergstedt, O and Nyström, K and Norder, H}, title = {Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70222}, doi = {10.1111/1758-2229.70222}, pmid = {41152000}, issn = {1758-2229}, support = {2020-02710//Svenska Forskningsrådet Formas/ ; 20-102//Svenskt Vatten/ ; }, mesh = {*Drinking Water/virology ; *Virome ; *Water Purification/methods ; *Viruses/genetics/classification/isolation & purification ; Sweden ; Metagenomics ; *Water Microbiology ; Genome, Viral ; Bacteriophages/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.}, } @article {pmid41114530, year = {2025}, author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N}, title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {43}, pages = {27450-27468}, doi = {10.1021/acs.jafc.5c07003}, pmid = {41114530}, issn = {1520-5118}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Phenylethyl Alcohol/analogs & derivatives/administration & dosage ; Humans ; Animals ; Male ; Mice ; Bacteria/classification/genetics/isolation & purification/drug effects/metabolism ; Middle Aged ; Female ; Adult ; *Fatty Liver/metabolism/drug therapy/microbiology ; Liver/metabolism/drug effects ; Feces/microbiology ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism/drug therapy ; }, abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.}, } @article {pmid41036845, year = {2025}, author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M}, title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.}, journal = {mSphere}, volume = {10}, number = {10}, pages = {e0023425}, doi = {10.1128/msphere.00234-25}, pmid = {41036845}, issn = {2379-5042}, mesh = {*Rhizosphere ; *Wetlands ; *Poaceae/virology ; Plant Roots/virology/microbiology ; Soil Microbiology ; *Virome ; *Viruses/classification/genetics/isolation & purification ; Biodiversity ; Metagenome ; }, abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.}, } @article {pmid41025782, year = {2025}, author = {Boyd, AI and Kafer, LA and F Escapa, I and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP}, title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.}, journal = {mSphere}, volume = {10}, number = {10}, pages = {e0049325}, doi = {10.1128/msphere.00493-25}, pmid = {41025782}, issn = {2379-5042}, support = {U19AI157981//National Institute of Allergy and Infectious Diseases/ ; U19AI144297//National Institute of Allergy and Infectious Diseases/ ; U19AI116497//National Institute of Allergy and Infectious Diseases/ ; F31AI172324//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Humans ; *Cytokines/metabolism/immunology ; *Organoids/microbiology/immunology ; Streptococcus pneumoniae/growth & development/immunology ; Staphylococcus aureus/growth & development/immunology ; *Nasal Mucosa/microbiology/immunology ; *Microbiota ; Epithelial Cells/microbiology/immunology ; }, abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.

IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.}, } @article {pmid40996044, year = {2025}, author = {Kwon, J and Correa, MA and Kong, Y and Pelletiers, W and Wade, M and Olson, D and Pettigrew, MM}, title = {Microbiome signatures of Clostridioides difficile toxin production and toxin gene presence: a shotgun metagenomic approach.}, journal = {mSphere}, volume = {10}, number = {10}, pages = {e0043525}, doi = {10.1128/msphere.00435-25}, pmid = {40996044}, issn = {2379-5042}, support = {NU50CK000488/CC/CDC HHS/United States ; }, mesh = {Humans ; *Clostridioides difficile/genetics ; *Bacterial Toxins/genetics ; Female ; Male ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; *Clostridium Infections/microbiology/diagnosis ; Aged ; Adult ; Anti-Bacterial Agents/therapeutic use ; Diarrhea/microbiology ; Aged, 80 and over ; }, abstract = {Clostridioides difficile is an opportunistic gastrointestinal pathogen capable of asymptomatic colonization and causes diseases ranging from diarrhea to pseudomembranous colitis. Accurate diagnosis of C. difficile infection (CDI) is challenging and critical for treatment and control. We hypothesized that gut microbiome profiles could help distinguish C. difficile colonized patients with diarrhea from those with true CDI. We analyzed 172 stool samples from individuals who tested glutamate dehydrogenase positive for C. difficile. Participants were categorized by toxin status (i.e., toxin positive or negative) and then further classified into three toxin groups based on the production of toxin, and if not produced, whether the C. difficile strain carried toxin-encoding genes. We examined associations between patient characteristics, prior antibiotics exposure, microbiome community structure and function, and toxin categories. Thirty-five percent of toxin-negative participants received antibiotics despite not meeting the criteria for true CDI. Enterococcus species were abundant in all groups. The relative abundance of E. faecalis was higher among individuals with prior antibiotics exposure. Alpha and beta diversity did not differ by toxin group. After controlling for prior antibiotics exposure and previous CDI episode, the abundance of Akkermansia muciniphila, Flavonifractor plautii, and Bifidobacterium adolescentis distinguished individuals with toxin-positive C. difficile. C. difficile abundance did not differentiate participants with true CDI from those who were colonized. We identified associations between the gut microbiome and C. difficile toxin gene presence and toxin production. These results highlight the potential for microbiome-informed diagnostics to improve CDI accuracy and guide treatment decisions.IMPORTANCEClostridioides difficile colonizes humans and causes diarrhea in community and hospital settings. C. difficile infection (CDI) is a toxin-mediated disease, and its diagnosis is challenging. The goal of this study was to determine whether differences in the gut microbiome could help distinguish between colonized individuals and those with CDI. We examined stool samples and data from 172 individuals categorized into three groups based on the detection of toxin and, if not detected, whether toxin-encoding genes were present in the C. difficile strain. We identified bacteria, such as Enterococcus faecalis, that were more abundant in people who had used antibiotics. While the diversity of the gut microbiome did not differ by toxin group, specific gut bacteria, antibiotic resistance genes, and metabolic pathways were associated with toxin group. Our findings suggest that considering the full gut microbiome and factors like past antibiotic use could help improve the diagnosis and treatment of CDI.}, } @article {pmid40967455, year = {2025}, author = {Arffman, RK and Folch, BA and Leonés-Baños, I and Altmäe, S}, title = {Gut feelings-the gut microbiome as a regulator of mental health in polycystic ovary syndrome.}, journal = {Fertility and sterility}, volume = {124}, number = {5 Pt 2}, pages = {931-947}, doi = {10.1016/j.fertnstert.2025.09.014}, pmid = {40967455}, issn = {1556-5653}, mesh = {Humans ; *Polycystic Ovary Syndrome/psychology/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; *Mental Health ; *Emotions ; Animals ; }, abstract = {IMPORTANCE: Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with reproductive, metabolic, and mental health comorbidities. The exact mechanisms of PCOS-related psychological distress and the role of the microbiome in the process remain unclear.

OBJECTIVE: To systematically review the current literature on the gut microbiome's association with mental health in women with PCOS and to review the possible mechanisms.

EVIDENCE REVIEW: A comprehensive literature search across the PubMed database until July 2025. Studies were included if they met the following criteria: observational/intervention studies; assessing microbiome through 16S ribosomal ribonucleic acid amplicon/16S ribosomal ribonucleic acid gene sequencing/metagenomics; comparing microbiome between women with and without PCOS; published from 2007 until 2025, and articles available online. The exclusion criteria were: language other than English or Spanish; reviews; abstracts/posters; case reports; full text not available, and duplicates. Two independent reviewers screened all titles and abstracts to determine eligibility, and discrepancies were resolved through discussion. The methodological quality and the potential risk of bias were assessed following the Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies.

FINDINGS: A total of 159 studies were identified and screened for title, abstract, and full text. Eight studies met the criteria (2 rodent, 6 human studies). The quality assessment indicated that half of the studies (4/8) presented a high risk of bias. Regardless of the limited number of studies and the low quality scores, all the studies highlighted the association of the gut microbiome in PCOS with mental health problems.

CONCLUSIONS AND RELEVANCE: Our review provides the first summary of the studies performed to date on the gut-brain axis in PCOS. Our review highlights that the current state of the research is rather preliminary, and the existing studies possess various limitations and often lack rigorous study design. Nevertheless, all the studies indicated an association between changes in gut microbiome and mental health indicators in PCOS. We also noted a consistent increase in Gram-negative bacteria in women with PCOS and mental health issues. More research is needed on humans with a bigger sample size, different ethnicities, and wider age groups to clarify the microbial patterns involved, and in parallel, the field should move from descriptive studies to mechanistic approaches.}, } @article {pmid40883892, year = {2025}, author = {Kanaan, G and Deming, JW}, title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf198}, pmid = {40883892}, issn = {1751-7370}, support = {//Benjamin Hall Conservation Genetics/ ; 325405//Research Council of Norway BREATHE project/ ; }, mesh = {*DNA Methylation ; *Bacteria/genetics/classification ; *Ice Cover/microbiology/virology ; *Microbiota ; Metagenome ; Arctic Regions ; *Viruses/genetics ; DNA, Viral/genetics ; DNA, Bacterial/genetics ; Seawater/microbiology ; Epigenesis, Genetic ; }, abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea-ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6 mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and nonadapted bacteria (Pelagibacter); e.g. in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea-ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.}, } @article {pmid41151807, year = {2025}, author = {Bontemps, Z and Abrouk, D and Moënne-Loccoz, Y and Hugoni, M}, title = {Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70112}, doi = {10.1111/1758-2229.70112}, pmid = {41151807}, issn = {1758-2229}, support = {//DRAC Nouvelle Aquitaine (Bordeaux, France)/ ; }, mesh = {*Caves/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota/genetics ; *Fungi/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Melanins/biosynthesis/genetics ; Carotenoids/metabolism ; Phylogeny ; }, abstract = {Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.}, } @article {pmid41150726, year = {2025}, author = {Ma, M and Li, Q and Wu, F and Zhu, B and Lu, H and Zhang, D and Łukasik, P and Hu, Y}, title = {Symbiotic solutions for colony nutrition: Conserved nitrogen recycling within the bacterial pouch of Tetraponera ants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {44}, pages = {e2514882122}, doi = {10.1073/pnas.2514882122}, pmid = {41150726}, issn = {1091-6490}, support = {32370448//MOST | National Natural Science Foundation of China (NSFC)/ ; 2243200009//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; }, mesh = {*Ants/microbiology/physiology/metabolism ; Animals ; *Symbiosis/physiology ; *Nitrogen/metabolism ; Microbiota/physiology ; Larva/microbiology/growth & development ; Amino Acids/metabolism ; *Bacteria/metabolism/genetics ; Urea/metabolism ; }, abstract = {While microbial symbioses are fundamental to the nutrition of many animal groups, current paradigms focus on symbiont functions at the host individual level. It remains unclear whether microbial symbioses can sustain colony-level fitness in social insects, whose ecological success depends on nutrient coordination across castes. Here, we investigate the specialized bacterial pouch, a symbiont-containing organ present exclusively in adult workers of Tetraponera nigra-group ants, revealing its crucial role in colony-wide nutrient provisioning. Using a combination of microscopy, amplicon and metagenomic sequencing, and [15]N-urea feeding experiments on four species in the group, we show that its adult-specific pouch-associated microbiota, primarily Tokpelaia, recycle nitrogen from urea and convert it into amino acids which are provisioned to adult workers and developing larvae. Disruption of this nitrogen-recycling symbiosis severely impairs larval growth and overall colony fitness. Our results show how caste-restricted microbial organs can centralize metabolic functions at the colony level, challenging individual-centric paradigms of host-microbe mutualism and providing insights into the pivotal role of microbial symbionts in superorganismal adaptation to nutritional constraints.}, } @article {pmid41148396, year = {2025}, author = {Xie, X and Ren, W and Zhou, W and Wang, Y and Zhu, H and Wu, Y and Lu, Q}, title = {Genetic prediction of the effect of gut microbiota on retinal vein occlusion via blood metabolites.}, journal = {International ophthalmology}, volume = {45}, number = {1}, pages = {447}, pmid = {41148396}, issn = {1573-2630}, support = {2024KY376//Medical Science and Technology Program of Zhejiang Province/ ; 2022L003//Ningbo Clinical Research Center for Ophthalmology/ ; 2016-370 S05//Ningbo Clinical Research Center for Ophthalmology and the Project of NINGBO Leading Medical & Health Disipline/ ; 2021Z054//Technology Innovation 2025 Major Project of Ningbo/ ; 2024Z233//Ningbo"Innovation Yongjiang 2035" Key Technology Breakthrough program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Retinal Vein Occlusion/genetics/blood/microbiology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; *Polymorphism, Single Nucleotide ; Biomarkers/blood ; }, abstract = {PURPOSE: Given the unclear causal relationship between gut microbiota (GM) and retinal vein occlusion (RVO) and the potential mediating role of blood metabolites, this study aims to investigate this causal link and the mediating effects of blood metabolites.

METHODS: Our Mendelian randomization (MR) study used data from genome-wide association studies pooled data, including 473 microbiota taxa (n = 5959), 233 blood metabolites (n = 136,016), and RVO cases and controls from the FinnGen consortium (cases, n = 775; controls, n = 308,633). We used bidirectional two-sample MR, multivariate MR, and mediation analysis to assess the causal association between GM and RVO.

RESULTS: By analyzing gut microbial metagenomic data with adjustment for confounding factors, we identified 1 taxon with significant causal association and 14 taxa with potential causal links to RVO, where Halomonadaceae remained after Bonferroni correction. Parallel analysis of blood metabolites revealed 18 causal associations (2 significant, 16 potential), with apolipoprotein A-I and creatinine retaining significance post-correction. Three GM taxa affected RVO through three blood metabolites. Caloranaerobacteraceae, Rhodococcus, and Citrobacter A affected RVO through Total cholesterol in HDL2, Apolipoprotein A-I, and phenylalanine, respectively. Apolipoprotein A-1 possessed the greatest mediated effect (5.6%) between Rhodococcus and RVO.

CONCLUSION: These findings provide new insights into the pathogenesis of RVO and may contribute to the development of new strategies for preventing the onset of RVO.}, } @article {pmid41145643, year = {2025}, author = {Karpęcka-Gałka, E and Zielińska, K and Frączek, B and Łabaj, PP and Kościółek, T and Humińska-Lisowska, K}, title = {High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37529}, pmid = {41145643}, issn = {2045-2322}, support = {39/PB/RID/2022//Ministerstwo Edukacji i Nauki/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Altitude ; Adult ; *Mountaineering/physiology ; Biomarkers/blood ; *Diet ; Young Adult ; }, abstract = {This study examined how high-altitude exposure and expedition-specific dietary changes influence gut microbiome composition, functional pathways, and their relationships with performance and health markers in alpinists. Seventeen male mountaineers (age 30.29 ± 5.8 years) participating in multi-week expeditions (> 3,000 MASL) were assessed before and after their climbs. Assessments included dietary intake analysis, blood and urine biomarkers, aerobic and anaerobic performance tests, and metagenomic sequencing of the gut microbiome. Bioinformatic and statistical analyses evaluated changes in microbiome composition and function and their correlations with physiological and dietary parameters. High-altitude exposure was associated with significant shifts in gut microbial composition and functional capacity. While the total number of bacterial species and functions remained stable, the glucose degradation pathway increased post-expedition. Participants with greater microbiome shifts showed improved performance and had richer baseline microbiomes. Pre-expedition, certain microbial functions were associated with vitamin B6 and C intake, while post-expedition correlations involved specific macronutrients and micronutrients. Additionally, some microbiome changes correlated with blood markers, indicating links to nutrient metabolism and electrolyte balance. The gut microbiome of alpinists adapts to extreme environmental stress and dietary changes, influencing metabolic, immune, and performance-related processes. Optimizing dietary strategies to support a beneficial microbiome profile may enhance resilience and performance in challenging high-altitude environments.}, } @article {pmid41145216, year = {2025}, author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM}, title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280550.125}, pmid = {41145216}, issn = {1549-5469}, abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.}, } @article {pmid41065113, year = {2025}, author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC}, title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {108}, number = {1}, pages = {84-97}, doi = {10.1177/13872877251376911}, pmid = {41065113}, issn = {1875-8908}, mesh = {Humans ; *Hispanic or Latino/psychology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Cognition/physiology ; Aged ; Middle Aged ; Cohort Studies ; Feces/microbiology ; White ; }, abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.}, } @article {pmid41142817, year = {2025}, author = {Lee, JY and Mahurkar-Joshi, S and Young, A and Labus, JS and He, B and Aja, E and Jacobs, JP and Volkmann, ER}, title = {Ultra-processed food intake is associated with increased gastrointestinal tract symptoms and alterations in gut microbiota in patients with systemic sclerosis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1610360}, pmid = {41142817}, issn = {1664-3224}, mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Adult ; Aged ; *Gastrointestinal Diseases/etiology/microbiology ; *Dysbiosis ; Feces/microbiology ; Food Handling ; Food, Processed ; }, abstract = {BACKGROUND: Alterations in the gastrointestinal (GI) microbiome (i.e., dysbiosis) are a feature of systemic sclerosis (SSc). Diet is a known modifier of the GI microbiome, and ultra-processed food (UPF) consumption has been associated with adverse changes in GI microbial composition. This study aimed to determine whether UPF consumption affects the GI microbiota and GI symptoms in patients with SSc.

METHODS: Adult SSc patients provided stool samples and completed both the Diet History Questionnaire II (DHQ-2) and the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0). Shotgun metagenomics were performed using the Illumina NovaSeq 6000 with a target depth of 10 million 150x2 sequences per sample. UPF items (N=54) on the DHQ-2 were identified using the NOVA scale of food classification, and UPF intake was calculated as gram-per-week consumption according to patient reported frequency. General linear models were created to identify differentially abundant species based on UPF consumption and to evaluate the relationship between UPF consumption and GI symptoms as measured by the GIT 2.0. These models adjusted for body mass index (BMI), current proton pump inhibitor (PPI) use, current probiotic use, current or prior immunomodulatory therapy, and presence of small intestinal bacterial overgrowth (SIBO).

RESULTS: Of the 65 total SSc patients included, 84.6% were female. The mean age was 53.83 ± 13.19 years, and the mean BMI was 25.25 ± 4.75. The median UPF consumption was 2395.82 g/week. Increased UPF consumption was significantly associated with increased GI symptoms in our multivariate model (β=0.34; p<0.01). Among 257 species analyzed, 5 bacterial species were significantly associated with UPF consumption in the multivariate models, including Limosilactobacillus fermentum (β=0.32; p<0.01) and Faecalicatena fissicatena (β= -0.36; p-value<0.01), while the abundance of 6 bacterial species was significantly associated with GI symptom severity after adjusting for the aforementioned covariates.

CONCLUSIONS: SSc patients reporting a higher UPF consumption demonstrated alterations in GI microbial composition as well as increased GI symptoms, even after adjusting for factors known to affect the microbiota of patients with SSc. Future studies are needed to determine whether interventions aimed at lowering UPF consumption may improve GI outcomes for patients with SSc.}, } @article {pmid41139486, year = {2025}, author = {Tran, T and Duong, DV and Le, TD and Bui, XT}, title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {10}, pages = {e70072}, doi = {10.1111/apm.70072}, pmid = {41139486}, issn = {1600-0463}, mesh = {*Biofilms/growth & development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; }, abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.}, } @article {pmid41138002, year = {2025}, author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M}, title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {178}, pmid = {41138002}, issn = {1572-9699}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.}, } @article {pmid41137523, year = {2025}, author = {Tegegne, HA and Savidge, TC}, title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2569739}, doi = {10.1080/19490976.2025.2569739}, pmid = {41137523}, issn = {1949-0984}, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; }, abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.}, } @article {pmid41137517, year = {2025}, author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S}, title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2568706}, doi = {10.1080/19490976.2025.2568706}, pmid = {41137517}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation & purification ; Models, Animal ; Disease Models, Animal ; }, abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.}, } @article {pmid41137068, year = {2025}, author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM}, title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.}, journal = {Parasites & vectors}, volume = {18}, number = {1}, pages = {426}, pmid = {41137068}, issn = {1756-3305}, mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.

METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Baños, Laguna, Philippines, that differ in topography and land use transformations.

RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.

CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.}, } @article {pmid41136898, year = {2025}, author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S}, title = {Prevalence of oxalotrophy in the human microbiome.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {954}, pmid = {41136898}, issn = {1471-2164}, support = {40B2-0_194701//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert Rüf Stiftung/ ; }, mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; }, abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.

RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.

CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.}, } @article {pmid41136439, year = {2025}, author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z}, title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9353}, pmid = {41136439}, issn = {2041-1723}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; }, abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.}, } @article {pmid40848995, year = {2025}, author = {Wang, J and Xue, L and Zhang, M and Shen, P and Zhao, W and Tong, Q and Wu, S and Dai, W and Yang, X and Wang, H}, title = {Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.}, journal = {Brain, behavior, and immunity}, volume = {130}, number = {}, pages = {106086}, doi = {10.1016/j.bbi.2025.106086}, pmid = {40848995}, issn = {1090-2139}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Parkinson Disease/therapy/microbiology ; Aged ; Double-Blind Method ; Quality of Life ; *Colonoscopy/methods ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome/physiology ; Constipation ; }, abstract = {OBJECTIVE: Growing evidence supports the efficacy and safety of fecal microbiota transplantation (FMT) in treating Parkinson's disease (PD). Fecal microbiota are commonly transplanted via oral capsules, a nasojejunal tube, or colonoscopy, but freezing often decreases the diversity and viability of transplanted microbiota. This single-center, double-blind, randomized, placebo-controlled trial aims to explore the efficacy and safety of fresh FMT via colonoscopy in dealing with PD.

METHODS: Thirty patients with mild-to-moderate PD (Hoehn-Yahr stage I-III) were randomly assigned into the FMT group (fresh FMT via colonoscopy) and placebo group (saline injection via colonoscopy) in a 1:1 ratio. Motor and non-motor symptoms, constipation, quality of life, cognitive function, emotional state and sleep quality were assessed using relevant scales. Fecal samples were harvested before and at 4, 8 and 12 weeks after treatment for metagenomic and metabolomics analyses.

RESULTS: A total of 30 patients with mild-to-moderate PD were enrolled in the present study, involving 18 males and 12 females with a median age of 68 years, a median age of onset of 63.5 years, and a median disease duration of 3 years. At 12 weeks, scores of the UPDRS Ⅲ (group × time effect, B =  - 8.80 [-13.79, -3.81]), PAC-QOL (group × time effect, B =  - 29.67 [-45.35, -13.98]), UPDRS Ⅱ (group × time effect, B =  - 5.07 [-8.85, -1.28]), NMSS (group × time effect, B =  - 35.60 [-53.59, -17.61]), PDQ-39 (group × time effect, B =  - 17.80 [-28.21, -7.39]), HAMA (group × time effect, B =  - 1.66 [-2.92, -0.40]), and HAMD (group × time effect, B =  - 1.33 [-2.49, -0.16]) were significantly reduced in the FMT group, while CSBM per week (group × time effect, B = 3.03 [1.42, 4.63]) and the Bristol Stool Scale score (group × time effect, B = 1.95 [0.12, 3.79]) significantly increased (all P < 0.05). Significant alterations were seen in the gut microbiota and fecal metabolites in the FMT group. No adverse events were observed during the follow-up period.

CONCLUSION: Fresh FMT via colonoscopy is a safe and well-tolerated procedure for treating mild-to-moderate PD. It effectively alleviates motor and non-motor symptoms, thus facilitating defecation and improving the quality of life. These effects can be maintained for a minimum of 12 weeks and may be attributed to the optimization of gut microbiota and fecal metabolites.}, } @article {pmid40835054, year = {2025}, author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q}, title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.}, journal = {Brain, behavior, and immunity}, volume = {130}, number = {}, pages = {106080}, doi = {10.1016/j.bbi.2025.106080}, pmid = {40835054}, issn = {1090-2139}, mesh = {Humans ; *Schizophrenia/virology/drug therapy/microbiology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/physiology ; *Virome/physiology ; Feces/virology ; Biomarkers ; Treatment Outcome ; Young Adult ; Antipsychotic Agents/therapeutic use ; }, abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.

METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.

RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR = 0.012), and two viral species were reduced in the low-response trajectory group.

CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.}, } @article {pmid41131658, year = {2025}, author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y}, title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {214}, pmid = {41131658}, issn = {2049-2618}, mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; }, abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.

RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15 days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.

CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.}, } @article {pmid41131656, year = {2025}, author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S}, title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {215}, pmid = {41131656}, issn = {2049-2618}, support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; }, mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metagenome ; }, abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.

RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.

CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.}, } @article {pmid41131583, year = {2025}, author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y}, title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1162}, pmid = {41131583}, issn = {1479-5876}, support = {No. CCCF-QF-2022B04-4//the China Crohn's & Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; }, abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.

METHODS: A cohort of treatment-naïve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.

RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p = 0.02) compared to HC, which was restored after EEN treatment at remission status (p < 0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r = 0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-α, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).

CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.}, } @article {pmid41131465, year = {2025}, author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N}, title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {683}, pmid = {41131465}, issn = {1471-2180}, mesh = {Tunisia ; *Salt-Tolerant Plants/microbiology ; *Endophytes/classification/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; DNA, Bacterial/genetics ; Soil/chemistry ; *Microbiota ; Salinity ; Biodiversity ; Sequence Analysis, DNA ; Amaranthaceae/microbiology ; }, abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.}, } @article {pmid41131078, year = {2025}, author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B}, title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37098}, pmid = {41131078}, issn = {2045-2322}, support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; }, mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention & control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; }, abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.}, } @article {pmid41101029, year = {2025}, author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L}, title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.}, journal = {Environment international}, volume = {204}, number = {}, pages = {109867}, doi = {10.1016/j.envint.2025.109867}, pmid = {41101029}, issn = {1873-6750}, mesh = {*Drinking Water/microbiology/parasitology ; *Amoeba/genetics/physiology ; *Drug Resistance, Microbial/genetics ; Symbiosis ; *Water Microbiology ; Bacteria/genetics ; Microbiota ; }, abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.}, } @article {pmid40889349, year = {2025}, author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K}, title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70039}, doi = {10.1111/1755-0998.70039}, pmid = {40889349}, issn = {1755-0998}, support = {2019-00275//Svenska Forskningsrådet Formas/ ; }, mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; }, abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.}, } @article {pmid40885278, year = {2025}, author = {Bastón-Paz, N and Moreno-Blanco, A and Palacios, E and Olavarrieta, L and Galeano, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oteo-Iglesias, J and López-Causapé, C and Fuentes, I and Oliver, A and Cantón, R and Del Campo, R and de Dios-Caballero, J}, title = {Exploring the complexities of intestinal and pulmonary microbiota in cystic fibrosis: A multi-omics approach.}, journal = {Respiratory medicine}, volume = {248}, number = {}, pages = {108331}, doi = {10.1016/j.rmed.2025.108331}, pmid = {40885278}, issn = {1532-3064}, mesh = {Humans ; *Cystic Fibrosis/microbiology/physiopathology ; Male ; Female ; Feces/microbiology ; Sputum/microbiology ; Adult ; *Gastrointestinal Microbiome/genetics ; *Lung/microbiology ; Metagenomics/methods ; Adolescent ; Fatty Acids, Volatile/metabolism/analysis ; Child ; Young Adult ; *Microbiota ; Multiomics ; }, abstract = {BACKGROUND: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).

METHODS: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.

RESULTS: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum. Viruses accounted for 0.4 % of the relative abundance in the gut and 0.6 % in lungs. Mycobacteroides abscessus was genetically identified in 10 individuals, although only 2 had positive cultures. Patients with higher levels of Pseudomonas filamentous phages had negative cultures for P. aeruginosa. The protozoan Toxoplasma gondii was detected in all sputum samples, accounting for 0.25 % of the metagenomic reads, with further PCR-confirmation in 50 % of subjects, including children. No correlation was found between SCFA and lung function or microbial composition. The resistome of the fecal compartment was higher than that of the lungs, and a greater abundance of SCFAs in the intestine was associated with poorer lung function.

CONCLUSIONS: Patients with normal-mild lung function had higher alpha diversity in the respiratory microbiota; however, beta diversity in the stool was statistically different compared with the group with poorer lung function. Although there were no differences in SCFA concentrations, butyrate-producing bacteria were more abundant in the sputum of the group with better lung function. In fecal samples, resistome to tetracyclines, glycopeptides, and aminoglycosides predominated, whereas in sputum an enrichment of ARGs related to tetracyclines, beta-lactams, and macrolides was observed.}, } @article {pmid40755083, year = {2025}, author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H}, title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.}, journal = {Molecular ecology resources}, volume = {25}, number = {8}, pages = {e70023}, doi = {10.1111/1755-0998.70023}, pmid = {40755083}, issn = {1755-0998}, support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; }, mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; }, abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).}, } @article {pmid40580061, year = {2025}, author = {Rathour, R and Ma, Y and Xiong, J and Wang, XW and Petersen, J and Zhang, X}, title = {Hemolymph microbiota and host immunity of crustaceans and mollusks.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf133}, pmid = {40580061}, issn = {1751-7370}, support = {//Synthetic Biology Research Centre of Shenzhen University/ ; //Austrian Science Fund/ ; //ERC Starting Grant EvoLucin/ ; 42476113//National Natural Science Foundation of China/ ; JCYJ20241202124403006//Shenzhen Science and Technology Program/ ; 2025A1515010475//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; }, mesh = {Animals ; *Hemolymph/microbiology/immunology ; *Microbiota/immunology ; Immunity, Innate ; *Mollusca/microbiology/immunology ; *Crustacea/microbiology/immunology ; }, abstract = {Crustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defense mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host's immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unraveling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustacean and mollusk species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.}, } @article {pmid41130610, year = {2025}, author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K}, title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.}, journal = {BMJ open respiratory research}, volume = {12}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003456}, pmid = {41130610}, issn = {2052-4439}, mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; }, abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.

METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.

RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.

CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.

PROSPERO REGISTRATION NUMBER: CRD42023436934.}, } @article {pmid41130083, year = {2025}, author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP}, title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118872}, doi = {10.1016/j.marpolbul.2025.118872}, pmid = {41130083}, issn = {1879-3363}, abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.}, } @article {pmid41122951, year = {2025}, author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH}, title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70062}, doi = {10.1111/1755-0998.70062}, pmid = {41122951}, issn = {1755-0998}, support = {//U.S. National Science Foundation/ ; }, abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.}, } @article {pmid41032862, year = {2025}, author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A}, title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.}, journal = {Journal of medicinal chemistry}, volume = {68}, number = {20}, pages = {21786-21806}, doi = {10.1021/acs.jmedchem.5c02169}, pmid = {41032862}, issn = {1520-4804}, mesh = {Humans ; *Thiazoles/pharmacology/chemistry/chemical synthesis ; *Colorectal Neoplasms/drug therapy/pathology/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; *Antineoplastic Agents/pharmacology/chemistry/chemical synthesis ; *Pyruvate Kinase/antagonists & inhibitors/metabolism ; *Membrane Proteins/antagonists & inhibitors/metabolism ; Cell Line, Tumor ; *Thyroid Hormones/metabolism ; Thyroid Hormone-Binding Proteins ; *Carrier Proteins/antagonists & inhibitors/metabolism ; Cell Proliferation/drug effects ; Structure-Activity Relationship ; Animals ; *Enzyme Inhibitors/pharmacology/chemistry ; }, abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.}, } @article {pmid41002268, year = {2025}, author = {Aminu, S and Ascandari, A and Benhida, R and Daoud, R}, title = {GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {10}, pages = {}, doi = {10.1093/bioinformatics/btaf548}, pmid = {41002268}, issn = {1367-4811}, support = {//Mohammed VI Polytechnic University/ ; //African Supercomputing Center at UM6P/ ; }, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Software ; *Metagenome ; Machine Learning ; Humans ; Cities ; }, abstract = {SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.

GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.}, } @article {pmid40613917, year = {2025}, author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M}, title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.}, journal = {Journal of gastroenterology}, volume = {60}, number = {11}, pages = {1384-1399}, pmid = {40613917}, issn = {1435-5922}, support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/genetics ; Biomarkers/blood/metabolism ; Middle Aged ; Metagenomics/methods ; Metabolomics/methods ; Poland ; Feces/microbiology/chemistry ; Case-Control Studies ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metabolome ; Disease Progression ; Young Adult ; Remission Induction ; }, abstract = {BACKGROUND & AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.

METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.

RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.

CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.}, } @article {pmid41122237, year = {2025}, author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT}, title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20232}, pmid = {41122237}, issn = {2167-8359}, mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Firmicutes/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; }, abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.}, } @article {pmid41121668, year = {2025}, author = {Enagbonma, BJ and Modise, DM and Babalola, OO}, title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.}, journal = {MicrobiologyOpen}, volume = {14}, number = {5}, pages = {e70085}, doi = {10.1002/mbo3.70085}, pmid = {41121668}, issn = {2045-8827}, support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; }, mesh = {*Sorghum/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fabaceae/growth & development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth & development ; *Edible Grain/growth & development/microbiology ; Agriculture/methods ; }, abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.}, } @article {pmid41121093, year = {2025}, author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S}, title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {447}, pmid = {41121093}, issn = {1478-811X}, support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; }, abstract = {BACKGROUND & AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.

METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.

RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.

CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.}, } @article {pmid41120531, year = {2025}, author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P}, title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36670}, pmid = {41120531}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; }, abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.}, } @article {pmid41005300, year = {2025}, author = {Zhao, CN and Li, SS and Yau, T and Chen, WQ and Ji, R and Guan, XY and Kong, FS}, title = {Phocaeicola vulgatus induces immunotherapy resistance in hepatocellular carcinoma via reducing indoleacetic acid production.}, journal = {Cell reports. Medicine}, volume = {6}, number = {10}, pages = {102370}, doi = {10.1016/j.xcrm.2025.102370}, pmid = {41005300}, issn = {2666-3791}, mesh = {*Carcinoma, Hepatocellular/microbiology/therapy/immunology/metabolism/pathology ; Humans ; *Indoleacetic Acids/metabolism ; *Liver Neoplasms/microbiology/therapy/immunology/metabolism/pathology ; Animals ; *Immunotherapy/methods ; Mice ; CD8-Positive T-Lymphocytes/immunology ; *Drug Resistance, Neoplasm ; Male ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; *Enterobacteriaceae ; Female ; }, abstract = {Immunotherapy has made remarkable achievements in various cancers, but response rates in hepatocellular carcinoma (HCC) remain highly variable. Understanding mechanisms behind this heterogeneity and identifying responsive patients are urgent clinical challenges. In this study, the metagenomic analysis of 65 HCC patients reveals distinct gut microbiota profiles distinguishing responders (Rs) from non-responders (NRs). These findings are further validated through fecal microbiota transplantation (FMT) in mouse models. Notably, Phocaeicola vulgatus (P. vulgatus) is enriched in NRs and diminishes anti-PD-1 efficacy in both syngeneic and orthotopic tumor models. Mechanistically, P. vulgatus suppresses the production of indoleacetic acid (IAA), thereby weakening interferon (IFN)-γ[+] and granzyme B (GzmB)[+]CD8[+] T cells and impairing the antitumor immune response. Furthermore, supplementation with IAA restores CD8[+] T cell cytotoxicity and counteracts the immune-suppressive effects of P. vulgatus. Our findings establish a causal relationship between P. vulgatus and anti-PD-1 resistance in HCC, highlighting IAA as a potential therapeutic target to enhance immunotherapy outcomes.}, } @article {pmid40985733, year = {2025}, author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM}, title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {10}, pages = {e0057425}, doi = {10.1128/aem.00574-25}, pmid = {40985733}, issn = {1098-5336}, mesh = {*Dioxanes/metabolism ; Biodegradation, Environmental ; *Bioreactors/microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/metabolism ; *Microbiota ; Phylogeny ; }, abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.

IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.}, } @article {pmid40981429, year = {2025}, author = {Ferretti, P}, title = {The gut remembers: the long-lasting effect of medication use on the gut microbiome.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0107625}, doi = {10.1128/msystems.01076-25}, pmid = {40981429}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology/adverse effects ; Electronic Health Records ; Proton Pump Inhibitors/pharmacology ; Feces/microbiology ; }, abstract = {Growing evidence suggests that antibiotics and many human-targeted medications can alter the gut microbiome composition, but the persistence of these effects remains unclear. In their article, Aasmets and colleagues (O. Aasmets, N. Taba, K. L. Krigu, R. Andreson, et al., mSystems e00541-25, 2025, https://doi.org/10.1128/msystems.00541-25) leveraged electronic health records (EHR) and stool metagenomic data from 2,509 individuals to assess the impact of past medication use (up to 5 years prior to sampling) on the gut microbiome composition. They found that nearly half of the 186 tested drugs had long-term effects, with antibiotics, beta-blockers, benzodiazepine derivatives, proton-pump inhibitors, and antidepressants associated with microbiome changes that persisted for years after intake. For some medications, the effects were additive, with greater impact observed after repeated use. Overall, the authors highlight how medication use in the years preceding sample collection represents an often overlooked confounding factor in microbiome studies and emphasize the utility of combining EHR with microbiome data to assess the impact of past medication use.}, } @article {pmid40980873, year = {2025}, author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR}, title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0060125}, doi = {10.1128/msystems.00601-25}, pmid = {40980873}, issn = {2379-5077}, support = {0054575-SuPAcow//Novo Nordisk Fonden/ ; 101000213//HORIZON EUROPE European Research Council/ ; FT230100560//Australian Research Council/ ; }, mesh = {Animals ; Cattle/microbiology ; *Methane/metabolism ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Animal Feed ; Bacteria/metabolism/genetics/classification ; }, abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.

IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.}, } @article {pmid40960303, year = {2025}, author = {Qie, J and Cao, M and Xu, M and Zhang, Y and Luo, L and Sun, C and Ke, D and Yuan, S and Jia, W and Qiu, T and Li, T and Du, X and Xiao, C and Hong, Z and Zhang, B}, title = {Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0109125}, doi = {10.1128/msystems.01091-25}, pmid = {40960303}, issn = {2379-5077}, mesh = {Humans ; *Hyperuricemia/microbiology/therapy ; *Gout/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Female ; Cohort Studies ; Uric Acid/metabolism ; Adult ; Aged ; Bacteria/genetics/classification ; Metagenomics ; }, abstract = {The gut microbiota plays a crucial role in the development of hyperuricemia (HUA) and gout. However, the variability in study designs and analytical methods has led to inconsistent conclusions across different studies. Here, we conducted a comprehensive analysis of the gut microbiota associated with HUA and gout by examining 368 16S rRNA sequencing data from four Chinese cohorts, including 159 healthy controls (HC), 136 HUA patients, and 73 gout patients. Our findings indicate that there were significant differences in the gut microbiota composition between the three groups. Specifically, the HUA and gout groups demonstrated an increased abundance of pro-inflammatory bacteria, such as Fusobacterium and Bilophila, while beneficial bacteria known for their anti-inflammatory properties and metabolic benefits, including Christensenellaceae R-7 group, Anaerostipes, and Collinsella, are relatively reduced. Additionally, we developed a predictive model using microbial markers that achieved a high accuracy (area under the curve [AUC] > 0.8) in distinguishing between the HC, HUA, and gout groups. Notably, further metagenomic analysis identified a species-level genome bin (SGB), designated as Phil1 sp00194085, belonging to the order Christensenellales. For the first time, we discovered that this SGB carries a uric acid metabolic gene cluster and possesses enzymes associated with purine metabolism, suggesting its potential role in uric acid metabolism. Overall, our study deepens the understanding of the gut microbiota's role in HUA and gout and lays a foundation for developing innovative therapeutic strategies to effectively control uric acid levels through gut microbiota modulation.In this study, we conducted a comprehensive analysis of gut microbiota across multiple cohorts, identifying distinct microbial signatures in healthy controls, hyperuricemia (HUA), and gout patients. We observed an increase in pro-inflammatory bacteria and a decrease in beneficial bacteria for host metabolism in both the HUA and gout groups. Additionally, we developed a predictive model with high accuracy (area under the curve [AUC] > 0.8) based on microbial markers and discovered a novel species with potential for uric acid metabolism, providing new therapeutic targets for HUA and gout.}, } @article {pmid40960301, year = {2025}, author = {Yan, Y and Zhao, X and Liang, X and Xue, Y and Niu, Q and Li, D and Zhou, X and Li, Y and Dong, S and Gai, Y}, title = {Global wastewater microbiome reveals core bacterial community and viral diversity with regional antibiotic resistance patterns.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0142824}, doi = {10.1128/msystems.01428-24}, pmid = {40960301}, issn = {2379-5077}, support = {BLX202162//Central University Basic Research Fund of China/ ; }, mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Microbial/genetics ; Humans ; Metagenome ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; Drug Resistance, Bacterial ; Biodiversity ; }, abstract = {Municipal wastewater treatment plants (WWTPs) serve as global repositories for diverse and dynamic microbial communities, reflecting the complex interplay of human activities, environmental conditions, and public health challenges. Despite their importance, a comprehensive understanding of the global distribution, composition, and functional roles of these microbial ecosystems has remained elusive. Here, we present a comprehensive analysis of bacterial and viral diversities in global wastewater systems by examining 575 sampling sites across 74 cities in 60 countries. Through metagenomic analysis, we reconstructed 12,758 non-redundant bacterial metagenome-assembled genomes (MAGs) spanning 70 phyla, with 4,499 MAGs representing novel species. Despite considerable regional variation, we identified a consistent core microbiome present across 70% of global samples predominantly comprising Proteobacteria. We further assembled 1.7 million viral genomes, revealing unprecedented viral diversity with over 1.5 million species-level viral operational taxonomic units (vOTUs). Network analysis demonstrated that transport proteins play crucial roles in maintaining WWTP functional resilience against disturbances. Machine learning approaches effectively predicted continental origins of wastewater samples based on microbial signatures, confirming that microbial communities reflect local environmental and socioeconomic conditions while maintaining functional conservation. We observed significant variation in the antibiotic resistance gene (ARG) distribution, with elevated prevalence in certain African and Asian regions compared to Europe and North America. Our results establish wastewater microbiomes as important indicators of human activity and provide critical insights for advancing environmental monitoring, antimicrobial resistance surveillance, and wastewater-based epidemiology.IMPORTANCEIntensifying urbanization and human activities have dramatically increased global wastewater generation, creating complex microbial ecosystems that significantly impact environmental and public health. This study presents the first large-scale, comprehensive characterization of bacterial and viral communities in wastewater treatment systems worldwide. By analyzing samples from diverse geographical, climatic, and socioeconomic contexts, we reveal how wastewater microbiomes serve as microbial fingerprints of human society, reflecting regional characteristics while maintaining functional conservation. Our findings demonstrate that these communities function as ecological extensions of human gut microbiota in the external environment, with important implications for the spread of antibiotic resistance and pathogens. The identification of viruses as key metabolic regulators in these systems provides new perspectives on microbial community dynamics. This global-scale analysis advances our understanding of wastewater microbiology and offers valuable insights for improving wastewater management, enhancing environmental monitoring systems, and strengthening public health surveillance through wastewater-based epidemiology.}, } @article {pmid40956075, year = {2025}, author = {Yu, D and Mai, Y and Zhang, L and Xiao, Y and Zhang, M and Shao, B and Chen, B and Wang, T and Zhang, K and Zhang, L and Gao, N and Zhang, J and Yan, J}, title = {Viral community succession during cadaver decomposition and its potential for estimating postmortem intervals.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {10}, pages = {e0145325}, doi = {10.1128/aem.01453-25}, pmid = {40956075}, issn = {1098-5336}, support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; }, mesh = {Cadaver ; Animals ; Rats ; *Postmortem Changes ; *Viruses/classification/genetics/isolation & purification ; *Microbiota ; Metagenomics ; }, abstract = {UNLABELLED: Microbial communities play a vital role in cadaver decomposition and serve as reliable tools for postmortem interval (PMI) estimation. However, current research focuses primarily on bacterial/fungal communities, though viruses-as Earth's most abundant biological entities-play key roles in biogeochemical cycles by regulating bacterial communities via lysis-lysogeny switching. Viral succession patterns during decomposition remain insufficiently characterized, and their PMI biomarker potential is unexamined. We present metagenomic analysis of viral succession during 35-day decomposition of buried rat cadavers, revealing stage-specific dynamics: early dominance of Peduoviridae (0-3 days), mid-stage proliferation of Herelleviridae (7-21 days), and late-stage resurgence of Peduoviridae (28-35 days). Viral α-diversity exhibits a fluctuating downward trend. β-Diversity analysis (PCoA, ANOSIM, PERMANOVA; P < 0.001) confirmed PMI as a major structural driver (27% variance explained). Nine viral families exhibited significant PMI correlations (P < 0.05): Zierdtviridae, Casjensviridae, Schitoviridae, and Ackermannviridae showed strong negative correlations (r = -0.82 to -0.78), while Straboviridae correlated positively (r = 0.59). Using integrated viral abundance data, our Extremely Randomized Trees model achieved exceptional PMI prediction accuracy (test set: R[2] = 0.96, MAE = 2.54 days). Spearman correlations between dominant bacterial phyla (Bacteroidota, Bacillota, etc.) and viral families, combined with Procrustes analysis (M[2] =0.3385, P = 0.001) and Mantel tests (r = 0.8059, P = 0.001), confirmed strong virus-bacteria community consistency. This indicates viruses may regulate decomposition by targeting bacteria for lysis, releasing nutrients (e.g., organic nitrogen/phosphorus) to drive bacterial succession. Our study establishes a novel virus-based PMI prediction tool and discusses ecological drivers of decomposition.

IMPORTANCE: We present a viral succession-based framework for estimating PMI in buried remains. Our study identifies stage-specific viral biomarkers and identified nine viral families significantly correlated with PMI. By combining metagenomics and machine learning, we developed an Extremely Randomized Trees (ERT) model that achieved a low prediction error (test set: R² = 0.96, MAE = 2.54 days). Furthermore, our findings demonstrate that viral and bacterial communities exhibit significant consistency and correlation during cadaver decomposition. This study not only provides a novel tool for the accurate estimation of forensic PMI but also advances our insight into viral regulation of bacteria and their interactions during cadaver decomposition.}, } @article {pmid40952003, year = {2025}, author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L}, title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0002325}, doi = {10.1128/msystems.00023-25}, pmid = {40952003}, issn = {2379-5077}, support = {2022-PUMCH-A-264//National High Level Hospital Clinical Reasearch Fungding/ ; 2022-PUMCH-A-042//National High Level Hospital Clinical Reasearch Fungding/ ; L232074//Natural Science Foundation of Beijing Municipality/ ; 2021-12M-C&TA-008//CAMS Innovation Funds for Medical Sciences/ ; 2022-PUMCH-C-031//National High Level Hospital Clinical Resarch Funding/ ; 2022-PUMCH-C-060//National High Level Hospital Clinical Research Funding/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; Adult ; *Polyps/microbiology/classification ; *Cervix Uteri/microbiology ; Metagenomics/methods ; Endometrium/microbiology/pathology ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.}, } @article {pmid40952001, year = {2025}, author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO}, title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0099125}, doi = {10.1128/msystems.00991-25}, pmid = {40952001}, issn = {2379-5077}, support = {988415//Crohn's and Colitis Foundation/ ; APP2011047//National Health and Medical Research Council/ ; Investigator grant//National Health and Medical Research Council/ ; Scientia fellowship//University of New South Wales/ ; }, mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Freeze Drying ; Female ; Male ; Administration, Oral ; Double-Blind Method ; Feces/microbiology ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; }, abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.

IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.}, } @article {pmid40928232, year = {2025}, author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS}, title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0103925}, doi = {10.1128/msystems.01039-25}, pmid = {40928232}, issn = {2379-5077}, mesh = {*Metagenomics/methods ; *Gene Library ; *Drug Resistance, Microbial/genetics ; Metagenome ; Biomass ; Bacteria/genetics ; Humans ; Microbiota/genetics ; }, abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.}, } @article {pmid40928220, year = {2025}, author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F}, title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0004425}, doi = {10.1128/msystems.00044-25}, pmid = {40928220}, issn = {2379-5077}, support = {No. 81670979,No. 31300424//National Natural Science Foundation of China/ ; 24-4-4-zrjj-158-jch//Natural Science Foundation of Qingdao Municipality/ ; ZR2024MH235//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; 202408010669//Shandong Medical and Health Technology Development Project/ ; }, mesh = {*Dental Caries/microbiology/diagnosis ; Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Child ; Female ; Male ; Child, Preschool ; }, abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.}, } @article {pmid40919923, year = {2025}, author = {Francis, JD and Yanaç, K and Uyaguari-Diaz, MI}, title = {Seasonal patterns of viromes in urban aquatic environments of Manitoba.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {10}, pages = {e0040824}, doi = {10.1128/aem.00408-24}, pmid = {40919923}, issn = {1098-5336}, support = {RGPIN-2022-04508//Natural Sciences and Engineering Research Council of Canada/ ; ALLRP 553987//Natural Sciences and Engineering Research Council of Canada/ ; 322388//University of Manitoba/ ; }, mesh = {Seasons ; Manitoba ; *Virome ; *Wastewater/virology ; *Rivers/virology ; *Water Microbiology ; Metagenomics ; *RNA Viruses/isolation & purification/genetics/classification ; Cities ; *DNA Viruses/isolation & purification/genetics/classification ; }, abstract = {UNLABELLED: Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as Autographiviridae, Kyanoviridae, and Peduoviridae, which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or "naked viruses" such as Partiviridae, Picobirnaviridae, Tombusviridae, and Picornaviridae, which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.

IMPORTANCE: Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.}, } @article {pmid40910778, year = {2025}, author = {Aasmets, O and Taba, N and Krigul, KL and Andreson, R and , and Org, E}, title = {A hidden confounder for microbiome studies: medications used years before sample collection.}, journal = {mSystems}, volume = {10}, number = {10}, pages = {e0054125}, doi = {10.1128/msystems.00541-25}, pmid = {40910778}, issn = {2379-5077}, support = {PRG1414//Eesti Teadusagentuur/ ; Installation grant 3573//European Molecular Biology Organization/ ; //Biocodex Microbiota Foundation/ ; 16-0125//Estonian Center of Genomics/Roadmap II/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Anti-Bacterial Agents/pharmacology/adverse effects ; Female ; Retrospective Studies ; Middle Aged ; Metagenomics/methods ; Adult ; Electronic Health Records ; Antidepressive Agents ; Aged ; Microbiota/drug effects ; }, abstract = {Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies. Recently, we and others showed that not only the usage of antibiotics and antidepressants at sampling, but also past consumption, is associated with the gut microbiome. This effect can be "additive"-the more a medication is used, the stronger the impact on the microbiome. Here, by utilizing retrospective medication usage data from the electronic health records and the observational Estonian microbiome cohort shotgun metagenomics data set (n = 2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome. We show that past usage of medications is associated with the gut microbiome. For example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after use. Furthermore, by analyzing a subcohort (n = 328) with a second microbiome characterization, we show that similar changes in the gut microbiome occur after treatment initiation or discontinuation, possibly indicating causal effects.IMPORTANCEThis is the first study using detailed retrospective medication usage data from electronic health records to systematically assess the long-term effects of medication usage on the gut microbiome. We identified carryover and additive effects on the gut microbiome for a range of antibiotics and non-antibiotic medications, such as benzodiazepine derivatives, antidepressants and glucocorticoids, among others. These findings highlight a collateral effect of diverse drug classes on the gut microbiome, which warrants accounting for long-term medication usage history when assessing disease-microbiome associations.}, } @article {pmid41117817, year = {2025}, author = {Gogoi, R and Bora, SS and Gogoi, B and Naorem, RS and Barooah, M}, title = {Insights into the microbial diversity and functionalities of potential hydrocarbon-degrading bioremediation agents in oil spill sludge of Assam, India.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {325}, pmid = {41117817}, issn = {1432-072X}, mesh = {India ; Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Petroleum Pollution/analysis ; *Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Surface-Active Agents/metabolism ; RNA, Ribosomal, 16S/genetics ; Petroleum/metabolism ; Phylogeny ; Biodiversity ; }, abstract = {Oil spill contamination poses a significant threat to environmental and ecological health, particularly in crude oil-rich regions such as Assam, a north-eastern state of India. This study explores the microbial diversity and functional potential of hydrocarbon-degrading bacteria in crude oil-contaminated sludge. Sludge samples were collected from three contaminated sites in Assam and analyzed for microbial diversity by culture dependent and independent (using 16 S rRNA amplicon sequencing) approaches. Metagenomic analysis revealed a diverse microbial community, with Proteobacteria and Planctomycetes dominating the metagenomes. Seven bacterial isolates, including Diaphorobacter nitroreducens, Lysinibacillus capsici, and Pseudomonas otitidis, were isolated and identified as potential hydrocarbon degraders. The isolates were screened and evaluated for biosurfactant production, hydrocarbon adhesion, and key enzymatic activities involved in degradation. These isolates exhibited significant biosurfactant-producing abilities, with Diaphorobacter nitroreducens MBRG1 showing the highest emulsification index (79%) and strong adherence to hydrocarbons. The enzymatic activities of alkane hydroxylase and alcohol dehydrogenase confirmed the metabolic capabilities of the isolates in hydrocarbon degradation. Optimal growth conditions for biosurfactant production were determined to be pH 7, 30 °C, 2% sucrose as the carbon source, and 3% yeast extract as the nitrogen source. The study highlights the potential of these indigenous bacterial isolates in bioremediation strategies to mitigate oil contamination. Future studies should focus on large-scale bioreactor studies, field trials, and strain improvement of these bacteria to enhance their degradation efficiency and adaptability to varied environmental conditions.}, } @article {pmid41115930, year = {2025}, author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK}, title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {199}, pmid = {41115930}, issn = {2055-5008}, support = {F31DE033564/DE/NIDCR NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; R03DE030527/DE/NIDCR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs & derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation & purification ; Microbiota ; Fusobacterium nucleatum/isolation & purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation & purification ; Porphyromonas gingivalis/isolation & purification ; }, abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.}, } @article {pmid40897099, year = {2025}, author = {Ma, X and Zhai, T and Bao, X and Wu, Z and Yang, Y and Yin, R and Cai, C and Liu, G}, title = {Salinity-driven trade-offs between nitrogen removal and microbiome dynamics in Fe-C-CWs toward saline aquaculture tailwater management.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124519}, doi = {10.1016/j.watres.2025.124519}, pmid = {40897099}, issn = {1879-2448}, mesh = {*Salinity ; *Nitrogen ; *Microbiota ; *Aquaculture ; Iron ; Denitrification ; }, abstract = {Salinity-driven nitrogen removal mechanisms in iron-carbon CWs (Fe-C-CWs) remain poorly understood for aquaculture tailwater management. Through a 155-day trial under four salinities (designated as S0, S10, S20, and S30), result showed that S20 achieved optimal removals of total nitrogen (84.9 ± 3.1 %), nitrate (81.8 ± 2.5 %), and ammonium (79.3 ± 3.0 %), significantly outperforming other groups (P < 0.05). Metagenomics revealed that S20 significantly enriched denitrifying taxa (Halothiobacillus, Prolixibacter) and upregulated nitrogen cycling genes (nirB, nrfA, nrfH, hao) and iron cycling genes (feoA, feoB), highlighting the functional synergy between microbial composition and biogeochemical cycling processes. Dual isotope signatures (δ[15]NNO2/ δ[18]ONO2) first applied in Fe-C-CWs confirmed salinity-mediated pathway shifts: nitrite oxidation dominated in saline groups, especially in S20 versus reduction in S0. Enzymatic profiling substantiated the concurrent operation of nitrification, denitrification, and anammox pathways across all groups, with activities exhibiting significant salinity-dependent modulation. S20 demonstrated remarkable enzymatic potentiation, where core nitrogen-cycling enzymes including nitrite oxidoreductase (NXR: 8.79 ± 0.67 U/g), nitrate reductase (NAR: 18.13 ± 1.19 U/g), and nitrite reductase (NIR: 6.74 ± 0.47 U/g) showed 16.00∼32.18 % higher than S0 (P < 0.01). This enzymatic synergy suggests salinity-optimized coupling between dissimilatory iron reduction and nitrogen transformation processes. Ecological network analysis revealed significant interactions among microbial phyla, particularly between Proteobacteria and Planctomycetota. This study demonstrates that S20 can enhance interaction between Fe-C matrix and microorganisms, thereby improving the efficiency of Fe-C-CWs in removing nitrogen pollutants from aquaculture tailwater. These findings offer theoretical insights for further understanding the internal operational mechanisms of the Fe-C-CWs.}, } @article {pmid40882565, year = {2025}, author = {Cheng, S and Hu, Y and Gu, X and Xu, X and Duan, X and Li, X and Liu, Z and Jian, Q and Oleskowicz-Popiel, P and Shen, P and Zhou, A and Xue, G and Makinia, J}, title = {Magnetite-enhanced chain elongation via endogenous electron donors through a novel fungi-bacteria microbiome.}, journal = {Water research}, volume = {287}, number = {Pt B}, pages = {124478}, doi = {10.1016/j.watres.2025.124478}, pmid = {40882565}, issn = {1879-2448}, mesh = {*Microbiota ; Bacteria/metabolism ; *Ferrosoferric Oxide ; Fungi/metabolism ; Fermentation ; Fatty Acids/metabolism ; }, abstract = {Anaerobic fermentation of organic waste stream into medium-chain fatty acids (MCFA) through chain elongation (CE) has emerged as a sustainable and eco-friendly approach for resource recovery. Co-culture of yeast with chain elongator achieved a promising endogenous electron donor (ED)-driven CE but was limited by the weak yeast-bacteria synergy. This study presents a novel approach to optimizing the CE process through the regulation of magnetite (0-15 g/L). Results indicated that the 5 g/L of magnetite (Mag-5) achieved MCFA production at 8.42±0.67 g COD/L, which was 2.01 times greater than the blank. In-situ ethanol and lactate served as the ED to drive the CE. Under the optimal condition (Mag-5), Streptococcus (55.83%) and Candida (57.52%) were the dominant ED-producing microorganisms, and Clostridium_sensu_stricto_12 (22.70%) was the dominant chain elongator. In addition, metagenome analysis demonstrated the enhancement in reverse β-oxidization for MCFA production. Furthermore, the truncated tricarboxylic acid cycle was enhanced by magnetite amendment to provide more reduced energy, potentially accelerating the electron transfer within the mixed fungi-bacteria consortia. Finally, the constructed network of fungi and bacteria discerned the substrate competition between yeast and bacteria, and the cooperation among chain elongators, yeast, and mold. This study first proposed to regulate the mixed fungi-bacteria microbiome with magnetite to enhance the in-situ ED-driven CE process, providing a viable approach to the bioconversion of organic streams into high-value products.}, } @article {pmid40834728, year = {2025}, author = {Bains, A and Dahal, S and Manna, B and Lyte, M and Yang, L and Singhal, N}, title = {L-norepinephrine induces community shift, oxidative stress response, metabolic reprogramming, and virulence potential in wastewater microbiomes.}, journal = {Water research}, volume = {287}, number = {Pt A}, pages = {124353}, doi = {10.1016/j.watres.2025.124353}, pmid = {40834728}, issn = {1879-2448}, mesh = {*Oxidative Stress/drug effects ; *Wastewater/microbiology ; Virulence/drug effects ; *Microbiota/drug effects ; *Bacteria/drug effects/pathogenicity/genetics/metabolism ; }, abstract = {Neuroendocrine compounds discharged into wastewater systems represent an emerging challenge at the intersection of human physiology and environmental microbiology. l-norepinephrine (L-NE), which has been recognized to potentiate growth of human and animal bacterial pathogens, is discharged in sewage through urine and faeces. While extensive pure culture studies have established l-NE's capacity to modulate bacterial virulence through iron acquisition and quorum sensing pathways, its impact on complex microbial communities, where intricate metabolic networks and interspecies interactions dominate, remains largely unexplored. This knowledge gap is particularly critical as urbanization drives increasing neuroendocrine compound loads in wastewater influents in metropolitan areas. Through parallel treatments of l-NE (1 × 10[-5] M to 1 × 10[-4] M), dextrose, and H2O2 in municipal and agricultural wastewater communities, we uncovered sophisticated metabolic and regulatory mechanisms that challenge the conventional understanding of microbial substrate utilization. Despite containing 10-fold less carbon, l-NE treatments achieved superior growth (10[8] CFU mL[-1]) while maintaining Pseudomonadaceae-dominated communities. Targeted metaproteomics revealed coordinated upregulation of oxidative stress genes (oxyR, soxRS) and antioxidant enzymes, while proteome-constrained metabolic modeling demonstrated distinct pathway modulation in central carbon and nitrogen metabolism. Notably, when compared to dextrose-supplemented controls, representing typical carbon substrate utilization, l-NE treatments showed similar taxonomic profiles without preferential enrichment of known pathogenic families. However, l-NE significantly enhanced autoinducer gene (luxS, qseC) expression, suggesting increased virulence potential through community-level metabolic reprogramming. These findings reveal l-NE as a potent modulator of microbial community dynamics in engineered ecosystems, with important implications for treatment process stability and downstream environmental impacts.}, } @article {pmid40784283, year = {2025}, author = {Zhao, J and Wang, Q and Zhao, Y and Guo, J and Ji, Z and Huang, Y and Shen, Q and Liu, Y and Bai, Y and Qi, W and Liu, H and Chen, Y}, title = {Chronic exposure to environmentally-relevant sulfamethoxazole alters ammonia-oxidizing microbial communities in managed aquifer recharge systems.}, journal = {Water research}, volume = {287}, number = {Pt A}, pages = {124298}, doi = {10.1016/j.watres.2025.124298}, pmid = {40784283}, issn = {1879-2448}, mesh = {*Sulfamethoxazole/pharmacology ; *Ammonia/metabolism ; *Groundwater/microbiology ; Archaea/drug effects ; Oxidation-Reduction ; Bacteria/metabolism/drug effects ; Anti-Bacterial Agents ; Microbiota/drug effects ; }, abstract = {Managed aquifer recharge (MAR) is a critical technology for water resource management and purification, yet its capacity to remove antibiotics remains limited. Understanding the response of ammonia-oxidizing microorganisms (AOMs) to antibiotics exposure is essential for optimizing MAR-based antibiotic mitigation strategies. This study investigated the long-term effects of sulfamethoxazole (SMX, ∼500 ng/L) on AOM communities through a 20-month controlled MAR column experiment. Results showed that AOMs (0.4-3.7 % of total microbial abundance) were dominated by ammonia-oxidizing archaea (AOA, 10.2-82.9 %) and complete ammonia oxidizers (comammox, 15.4-89.7 %), with negligible ammonia-oxidizing bacteria (AOB, <2.4 %). Chronic effects of SMX resulted in a 60-67 % reduction in amoA genes across AOA, AOB, and comammox populations, indicating a significant threat to nitrogen cycling. Specifically, SMX suppressed 2-7 AOA metagenome-assembled genomes (MAGs) (e.g., Nitrosotenuis) by 57-95 % and 4-5 comammox MAGs (e.g., Nitrospira) by 23-82 %. Conversely, SMX increased 4-7 AOA MAGs (e.g., Nitrosarchaeum) by 1.4-24.3-fold and 2 comammox MAGs (e.g., Nitrospira) by 1.9-2.0-fold, revealing taxon-specific tolerance. Notably, AOA lineages demonstrated superior resilience to SMX compared to comammox. These findings advance our understanding of antibiotic-driven microbial community dynamics in MAR systems and provide valuable insights for enhancing their performance in antibiotic-polluted environments.}, } @article {pmid41115834, year = {2025}, author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK}, title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70216}, doi = {10.1111/1758-2229.70216}, pmid = {41115834}, issn = {1758-2229}, support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; }, mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation & purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.}, } @article {pmid41112778, year = {2025}, author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W}, title = {Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20170}, pmid = {41112778}, issn = {2167-8359}, mesh = {Animals ; *Crows/virology ; *Feces/virology ; *Virome/genetics ; *DNA, Viral/genetics ; *DNA Viruses/genetics/isolation & purification/classification ; Metagenomics ; }, abstract = {As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.}, } @article {pmid41112578, year = {2025}, author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X}, title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1594460}, pmid = {41112578}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation & purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; }, abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.

METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.

RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.

CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.}, } @article {pmid41112258, year = {2025}, author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP}, title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1679071}, pmid = {41112258}, issn = {1664-3224}, mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; }, abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.

METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.

RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.

CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.}, } @article {pmid41112045, year = {2025}, author = {Zhang, Y and Gilbert, JA and Liu, X and Nie, L and Xu, X and Gao, G and Lyu, L and Ma, Y and Fan, K and Yang, T and Zhang, Y and Zhang, J and Chu, H}, title = {SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils.}, journal = {iMeta}, volume = {4}, number = {5}, pages = {e70058}, pmid = {41112045}, issn = {2770-596X}, abstract = {Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%-99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10[4] cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.}, } @article {pmid41102734, year = {2025}, author = {Lv, Y and Zhang, L and Zhang, Y}, title = {Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {208}, pmid = {41102734}, issn = {2049-2618}, support = {42306104//National Natural Science Foundation of China/ ; 42122043//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute/ ; 21TQ1400201//Shanghai Jiao Tong University, Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; }, mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Geologic Sediments/microbiology ; Metagenome ; Ecosystem ; Microbiota ; Metagenomics/methods ; Phylogeny ; Nitrogen Cycle ; }, abstract = {BACKGROUND: The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.

RESULTS: We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48 × (nxrA) and 1.28 × (aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.

CONCLUSION: Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.}, } @article {pmid40812483, year = {2025}, author = {Han, Q and Xia, S and Huang, X and He, J and Yin, Y and Yin, J}, title = {Age-Related Differences in the Gut Microbiota of Pigs Influence Fat Deposition in the Mouse.}, journal = {The Journal of nutrition}, volume = {155}, number = {10}, pages = {3547-3561}, doi = {10.1016/j.tjnut.2025.07.022}, pmid = {40812483}, issn = {1541-6100}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; Swine ; Feces/microbiology ; Age Factors ; Lipid Metabolism ; *Adipose Tissue/metabolism ; RNA, Ribosomal, 16S/genetics ; *Aging ; Male ; Fecal Microbiota Transplantation ; }, abstract = {BACKGROUND: The gut microbiota significantly influences lipid metabolism, but the impact of its developmental patterns at different growth stages on fat deposition remains unclear.

OBJECTIVES: This study aimed to explore the dynamic changes in microbial diversity and composition during the growth of pig models and assess their involvement in fat deposition.

METHODS: Forty-five Duroc-Landrace-Yorkshire (DLY) crossbred pigs were killed at 5 ages: 90, 120, 150, 180, and 210 d of age (n = 9). Fecal samples were collected 1 and 15 d before each killing, and the fecal microbiota were detected by 16S rRNA sequencing. The backfat thickness, serum lipid concentrations, intramuscular fat, and fatty acid content in the longissimus dorsi muscle of pigs were measured to assess lipid metabolism. Fecal microbiota transplantation (FMT) from DLY pigs of different ages to antibiotics-challenged mice (n = 8) was used to confirm the effects of microbial development on fat deposition. Metagenomic sequencing was conducted on feces from pigs aged 150 and 180 d and their corresponding transplanted mice to identify key strains involved in fat deposition.

RESULTS: We observed marked alterations and an increase in intestinal microbial α-diversity with age, peaking at 150 d of age in DLY pigs (P < 0.05). Spearman correlation analyses indicated that 20 genera significantly correlated with the muscle fatty acid contents (P < 0.05). FMT further confirmed that the developmental patterns of the gut microbiota affected host fat deposition, with notable differences observed between the fecal microbiota at day 150 and 180 of age in pigs. Schaalia canis was identified as a potential key microbial strain involved in the developmental patterns of the gut microbiota-governed fat deposition, and its colonization in mice reduced fat deposition by downregulating of LXRα/β gene expressions (P < 0.05).

CONCLUSIONS: Gut microbiota development impacts fat deposition in pigs, with S canis capable of inhibiting fat deposition.}, } @article {pmid40790086, year = {2025}, author = {Wu, L and Lian, W and Bai, R and Chen, H and Wu, J and Li, H and Zhao, L}, title = {METTL3 facilitates colorectal cancer growth through altering the abundance of intestinal Akkermansia muciniphila.}, journal = {Cancer gene therapy}, volume = {32}, number = {10}, pages = {1098-1106}, pmid = {40790086}, issn = {1476-5500}, support = {82203607//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M721540//China Postdoctoral Science Foundation/ ; 2021A1515111186//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2024A04J6605//Guangzhou Municipal Science and Technology Project/ ; }, mesh = {*Colorectal Neoplasms/pathology/genetics/metabolism/microbiology ; Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; *Methyltransferases/metabolism/genetics ; Akkermansia ; Cell Line, Tumor ; }, abstract = {Colorectal cancer (CRC) is a prevalent malignant tumor that poses a significant threat to human health; however, the precise mechanism underlying its onset remains elusive. In this study, we utilized metagenomic sequencing to reveal the dysregulation of intestinal microbiota caused by CRC. Single-cell sequencing data showed elevated mRNA expression of methyltransferase-like protein 3 (METTL3) in CRC, which was correlated with the abundance of intestinal microbiota. Furthermore, we found that METTL3 promotion of CRC progression is microbiota-dependent. Using induced METTL3[fl/fl] Vil1-cre[+/-] mice, we identified the microbiota regulated by METTL3 in CRC. Our research indicates that METTL3 leads to high expression of HIF1α, which promotes the expression of lipocalin 2 (LCN2) in CRC cells, inhibiting the abundance of Akkermansia muciniphila, thereby promoting CRC progression.}, } @article {pmid41038565, year = {2025}, author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L}, title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.}, journal = {Life sciences}, volume = {381}, number = {}, pages = {124006}, doi = {10.1016/j.lfs.2025.124006}, pmid = {41038565}, issn = {1879-0631}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Infant, Newborn ; *Metagenome/genetics ; Cesarean Section ; Male ; Delivery, Obstetric ; Feces/microbiology ; Pregnancy ; }, abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.}, } @article {pmid40992653, year = {2025}, author = {Sharma, SP and Cha, MG and Kwon, GH and Song, SH and Park, JH and Kim, MJ and Eom, JA and Lee, KJ and Yoon, SJ and Park, H and Won, SM and Oh, KK and Ham, YL and Baik, GH and Kim, DJ and Suk, KT}, title = {Phocaeicola plebeius oral treatment improve fibrosis by reversing cirrhosis-related hepatic gene dysregulation.}, journal = {Life sciences}, volume = {381}, number = {}, pages = {123979}, doi = {10.1016/j.lfs.2025.123979}, pmid = {40992653}, issn = {1879-0631}, mesh = {Animals ; *Liver Cirrhosis/genetics/microbiology/drug therapy ; Humans ; Mice ; Male ; Gastrointestinal Microbiome/drug effects ; Female ; Gene Expression Regulation/drug effects ; Liver/metabolism/pathology ; Middle Aged ; Administration, Oral ; Dysbiosis ; *Bacteroidetes ; Feces/microbiology ; }, abstract = {BACKGROUND: Bacteroides-centric gut dysbiosis reported to exacerbates liver cirrhosis via inflammation and fibrosis, therefore utilizing Bacteroides species as microbiome-based therapeutic logical to mitigate disease progression.

MATERIALS AND METHODS: Feces were collected from 52 Healthy and 144 Liver cirrhosis individuals for V3-V4 dependent 16rRNA-bsed comparative metagenomics analysis, followed a by microbiome depleted and non-depleted DDC mice model to explain the role of Bacteroidetes phylum classified microbial species P. plebeius in liver fibrosis pathophysiological pathways.

RESULTS: Bacteroides presented cirrhosis-dependent decrease in human and animal microbiome, and negatively correlated to key molecular pattern associated with cirrhosis. P. plebeius significantly reduced in abundance and identified as a microbial biomarker for cirrhosis (AUC = 0.73) and treatment with P. plebeius significantly improved the levels of cirrhosis-related phenotypical and biochemical markers in the microbiome-depleted cirrhosis group. P. plebeius decrease the expression of S100a9, CCR1, ADAM8, TREM2, ITGAM, and MYO5A which are primarily responsible for inducing inflammation in liver cirrhosis. P. plebeius downregulated the fibrosis related genes expression including CD51, PLAT, ITGA3, CXCR4, and TGFBR1 and gene related to extracellular matrix formation including COL1A1, LTBP2, S100A6, and SMCO2. Additionally, P. plebeius treatment decreased the expression of hepatotoxicity-related genes including LPL, KRT18, ALDOA, and MCM10, and increased the expression of FABP1 and RDX. Additionally, P. plebeius normalized the expression of genes connected to two pathophysiological process including TIMP4, TGFB3, S100A8, PLSCR1, MMP8, CXCL4, and BMP.

CONCLUSIONS: Our study revealed P. plebeius as a multifaceted bio-therapeutic candidate that normalized dysregulated gene expression and reversed hepatic inflammation, fibrogenesis, and hepatotoxicity.}, } @article {pmid41102233, year = {2025}, author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF}, title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36158}, pmid = {41102233}, issn = {2045-2322}, support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; }, mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; }, abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.}, } @article {pmid40846194, year = {2025}, author = {Han, Y and Cui, J and Guo, P and Yang, S}, title = {Remediation effects of straw combined with microbial agents on cinnamon soils with varying degradation based on metagenomics and untargeted metabolome.}, journal = {Environmental research}, volume = {285}, number = {Pt 5}, pages = {122649}, doi = {10.1016/j.envres.2025.122649}, pmid = {40846194}, issn = {1096-0953}, mesh = {*Soil Microbiology ; Metagenomics ; *Cinnamomum zeylanicum ; *Metabolome ; Soil/chemistry ; Biodegradation, Environmental ; *Environmental Restoration and Remediation/methods ; *Soil Pollutants/metabolism ; Microbiota ; }, abstract = {Microbial agents show potential for improving soil quality and crop yield. However, in the context of different soil degraded degrees, the effects of straw combined with microbial agents on soil microbial communities and their associated metabolic processes remain insufficiently explored. Here, we conducted pot experiments using cinnamon soils at three degradation levels (highly, moderately, and non-degraded), applying straw alone or straw combined with microbial agents during alfalfa cultivation. In this study, we combined metagenomic sequencing and untargeted metabolomics to study the effects of straw and straw combined with microbial agents on soil quality and plant biomass, and metabolites as well as on the network complexity and stability of soil microbial communities. Our findings showed that both straw and straw-microbial agent combinations enhanced the soil quality and alfalfa yield, as well as on the complexity and stability of bacterial networks in highly degraded soils. Meanwhile, the straw-microbial agent combination significantly altered key metabolic pathways (e.g., steroid hormone biosynthesis, cofactor biosynthesis, and nucleotide metabolism) and differentially regulated metabolites (e.g., amino acids/peptides, organosulfur compounds, and alkaloids) compared to straw alone, with distinct effects observed across degradation levels. Overall, the microbial community and their metabolites shaped by straw and straw combined with microbial agents promoted the remediation of degraded soils, ultimately enhancing soil quality and plant biomass. These findings advance the understanding of straw and microbial agents as a synergistic remediation strategy for modulating soil microbial communities and offer practical insights for soil health restoration.}, } @article {pmid40774558, year = {2025}, author = {Li, Y and Dai, L and Zhang, L and Shen, X and Zhang, X and Yang, Y and Guan, Y}, title = {Metagenomic insights into the changes of runoff water quality in a deep tunnel drainage system.}, journal = {Environmental research}, volume = {285}, number = {Pt 3}, pages = {122509}, doi = {10.1016/j.envres.2025.122509}, pmid = {40774558}, issn = {1096-0953}, mesh = {*Water Quality ; China ; Water Pollutants, Chemical/analysis ; Rain ; Metagenomics ; Environmental Monitoring ; Microbiota ; *Water Microbiology ; *Metagenome ; Nitrogen ; }, abstract = {Deep tunnel retrofitting of conventional urban drainage systems represents a pivotal strategy for mitigating stormwater pollution and combating flooding. While microbial-driven biogeochemical cycles in stormwater are constrained by taxonomic diversity and environmental variability, the interplay between hydrogeochemical dynamics and microbial functional genes during storage remains poorly characterized. In this study, an in situ stormwater self-purification system was constructed to investigate seasonal water quality evolution, microbial community dynamics, and functional gene regulation in Shenzhen, China. Compared with continuous rainfall events, initial postdrought stormwater events resulted in significantly elevated pollutant loads. Dissolved organic matter analysis revealed that endogenous contaminants accounted for 76 % of the total contaminants, characterized by high microbial bioavailability and low humification after 14 days of storage. The storage of samples favors the enrichment of functional microorganisms such as Plancomycetota, Verrucomicrobiota and Proteobacteria. A quantitative assessment of 62 functional genes linked to carbon (C)/nitrogen (N)/sulfur (S) cycling identified temperature, oxidation‒reduction potential ammonia nitrogen, chemical oxygen demand and total nitrogen as critical drivers of microbial community succession and gene abundance. N cycle genes presented heightened sensitivity to environmental fluctuations, with increased stability and metabolic activity observed in wet season samples. Comparative analysis demonstrated that deep tunnel samples presented more stable functional gene profiles and enriched microbial consortia relative to their surface counterparts. These findings elucidate the mechanistic relationships between hydrogeochemical variables and microbial functional resilience in stormwater storage systems. This work advances the process-level understanding of biochemical cycles mediated by C, N and S transformations, offering actionable insights for optimizing urban drainage infrastructure and microbial-mediated pollution control strategies.}, } @article {pmid40617568, year = {2025}, author = {Tian, G and Zhang, R and Zhao, M and Ye, Z and Dai, T and Chen, D and Zeng, Y and Yang, Y and Zhou, J and Zhang, B and Guo, X}, title = {Biogeochemical stratification governs microbial hydrocarbon degradation potential in a petrochemical contaminated site.}, journal = {Environmental research}, volume = {285}, number = {Pt 1}, pages = {122286}, doi = {10.1016/j.envres.2025.122286}, pmid = {40617568}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Petroleum/metabolism ; Groundwater/chemistry/microbiology ; Petroleum Pollution ; Microbiota ; Bacteria/metabolism ; }, abstract = {The success of in situ bioremediation at petrochemical-contaminated sites (defined as those impacted by petrochemical production or accidental release) depends on the structure and functional capacities of indigenous microbial communities, as well as the physicochemical gradients that shape their metabolic potential. While microbial degradation mechanisms are well-documented in homogeneous environments, systematic evaluations of microbial dynamics across environmental compartments (e.g., surface/middle/deep soil vs. groundwater) remain scarce. In this study, we combined chemical profiling with shotgun metagenomic sequencing to characterize layer-specific microbial assemblages and hydrocarbon degradation pathways at a historically contaminated petrochemical site. Total petroleum hydrocarbons (TPHs) were markedly higher in the middle and deep soil layers compared to the surface. In subsurface layers, elevated organic carbon and moisture limited oxygen diffusion, and high concentrations of hydrophobic hydrocarbons imposed toxic stress, together creating a reducing environment that favored anaerobic taxa and pathways such as benzoyl-CoA reductase. In contrast, surface soils, with greater aeration and lower pollutant levels, harbored approximately 50 % greater microbial α-diversity (P < 0.05) and supported more diverse and complex metabolic capabilities. Groundwater showed an 83 % detection frequency of naphthalene, and its high solubility and toxicity selected for specialized degraders. Principal Coordinates Analysis (PCoA) revealed distinct depth-dependent community clustering of microbial communities (P < 0.001), with middle/deep soil microbiomes showing significantly reduced metabolic versatility for xenobiotics (BTEX, PAHs, and derivatives) compared to surface soils and groundwater at the community level. Functional gene annotation identified rate-limiting enzymes in aerobic/anaerobic degradation pathways (dmpK [benzene], badA [ethylbenzene], nahA [naphthalene], and fadA [fatty acid β-oxidation]), and Metagenome-Assembled Genomes (MAGs)-based reconstructions revealed a systemic bias towards anaerobic degradation. These mechanistic insights guide layer-specific in situ bioremediation, integrate environmental gradients with microbial functional potential for targeted treatments, and provide a framework for predicting community succession and functional resilience at petrochemical-contaminated sites.}, } @article {pmid40209695, year = {2025}, author = {Yamane, T and Masaoka, T and Ishii, C and Masuoka, H and Suda, W and Kurokawa, S and Kishimoto, T and Mikami, Y and Fukuda, S and Kanai, T}, title = {Factors Contributing to the Efficacy of Fecal Microbiota Transplantation for Diarrhea-Dominant Functional Bowel Disorders.}, journal = {Digestion}, volume = {106}, number = {5}, pages = {469-479}, doi = {10.1159/000545183}, pmid = {40209695}, issn = {1421-9867}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Diarrhea/therapy/microbiology/etiology ; Female ; Feces/microbiology/chemistry ; Male ; Middle Aged ; Adult ; Treatment Outcome ; Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/therapy/microbiology ; Dysbiosis/therapy/microbiology ; Aged ; }, abstract = {INTRODUCTION: In cases of effective fecal microbiota transplantation (FMT) for irritable bowel syndrome (IBS), donor feces have been observed to be enriched in Bifidobacterium spp. Moreover, FMT for functional bowel disease can improve psychiatric symptoms. Although intestinal dysbiosis has received attention as one of the pathophysiologies of IBS, the efficacy of FMT for IBS has not yet been established. In this study, we performed a post hoc analysis of the efficacy of FMT, focusing on metabolites in donor feces.

METHODS: FMT was performed in 12 patients, 8 with refractory diarrhea-predominant IBS and 4 with functional diarrhea (FDr), who were refractory to medical therapy. The donors were family members within a second degree of kinship and differed for each transplant. Fecal characteristics were evaluated before and 12 weeks after transplantation using the Bristol stool scale (BS). BS scores of 3-5 at 12 weeks after transplantation were considered to indicate responders, while BS scores of 6 and 7 indicated nonresponders. Metagenomic and metabolomic analyses of all 12 donor fecal samples were performed to compare the responder and nonresponder groups.

RESULTS: Before transplantation, all patients had BS scores of 6-7, but 12 weeks after transplantation, 6 were considered responders and 6 were nonresponders. Metagenomic analysis showed that effective donor feces contained significantly higher levels of Prevotella than did the ineffective donor feces. Metabolomic analysis showed that effective donor feces contained significantly higher levels of propionate and butyrate and significantly lower lactate levels than did ineffective donor feces.

CONCLUSION: Propionate-, butyrate-, or Prevotella-rich donor feces may contribute to successful FMT in patients with diarrhea-dominant functional gastrointestinal disorders.}, } @article {pmid41100443, year = {2025}, author = {Shi, F and Zou, D and Zhang, L and Guo, N and Yu, J and Degen, AA and Tang, X and Ren, S and Ru, Y and Zheng, S and Zhang, Y and Wang, D}, title = {Increased urea nitrogen salvaging by a remodeled gut microbiota helps nonhibernating pikas maintain protein homeostasis during winter.}, journal = {PLoS biology}, volume = {23}, number = {10}, pages = {e3003436}, doi = {10.1371/journal.pbio.3003436}, pmid = {41100443}, issn = {1545-7885}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Nitrogen/metabolism ; *Urea/metabolism ; Seasons ; *Lagomorpha/metabolism/microbiology/physiology ; Homeostasis ; *Proteostasis/physiology ; Feces/microbiology ; Diet, Protein-Restricted ; Male ; Liver/metabolism ; Herbivory ; Fecal Microbiota Transplantation ; }, abstract = {Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.}, } @article {pmid41099510, year = {2025}, author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C}, title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0120825}, doi = {10.1128/msystems.01208-25}, pmid = {41099510}, issn = {2379-5077}, abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.

IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.}, } @article {pmid41097145, year = {2025}, author = {Tuigunov, D and Sinyavskiy, Y and Nurgozhin, T and Zholdassova, Z and Smagul, G and Omarov, Y and Dolmatova, O and Yeshmanova, A and Omarova, I}, title = {Precision Nutrition and Gut-Brain Axis Modulation in the Prevention of Neurodegenerative Diseases.}, journal = {Nutrients}, volume = {17}, number = {19}, pages = {}, doi = {10.3390/nu17193068}, pmid = {41097145}, issn = {2072-6643}, support = {Grant No. AP23489983//This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Neurodegenerative Diseases/prevention & control/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain ; *Precision Medicine/methods ; *Brain-Gut Axis/physiology ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; }, abstract = {In the recent years, the accelerating global demographic shift toward population aging has been accompanied by a marked increase in the prevalence of neurodegenerative disorders, notably Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Among emerging approaches, dietary interventions targeting the gut-brain axis have garnered considerable attention, owing to their potential to modulate key pathogenic pathways underlying neurodegenerative processes. This review synthesizes current concepts in precision nutrition and elucidates neurohumoral, immune, and metabolic regulatory mechanisms mediated by the gut microbiota, including the roles of the vagus nerve, cytokines, short-chain fatty acids, vitamins, polyphenols, and microbial metabolites. Emerging evidence underscores that dysbiotic alterations contribute to compromised barrier integrity, the initiation and perpetuation of neuroinflammatory responses, pathological protein aggregations, and the progressive course of neurodegenerative diseases. Collectively, these insights highlight the gut microbiota as a pivotal target for the development of precision-based dietary strategies in the prevention and mitigation of neurodegenerative disorders. Particular attention is devoted to key bioactive components such as prebiotics, probiotics, psychobiotics, dietary fiber, omega-3 fatty acids, and polyphenols that critically participate in regulating the gut-brain axis. Contemporary evidence on the contribution of the gut microbiota to the pathogenesis of Alzheimer's disease, Parkinson's disease, and multiple sclerosis is systematically summarized. The review further discusses the prospects of applying nutrigenomics, chrononutrition, and metagenomic analysis to the development of personalized dietary strategies. The presented findings underscore the potential of integrating precision nutrition with targeted modulation of the gut-brain axis as a multifaceted approach to reducing the risk of neurodegenerative diseases and preserving cognitive health.}, } @article {pmid41094699, year = {2025}, author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M}, title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {204}, pmid = {41094699}, issn = {2049-2618}, support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; }, mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; }, abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.

RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (> 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.

CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.}, } @article {pmid41093983, year = {2025}, author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR}, title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36025}, pmid = {41093983}, issn = {2045-2322}, support = {NIH R35 award GM152079/NH/NIH HHS/United States ; }, mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists & inhibitors/metabolism ; Sex Characteristics ; }, abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.}, } @article {pmid41091222, year = {2025}, author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY}, title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.}, journal = {Medical microbiology and immunology}, volume = {214}, number = {1}, pages = {49}, pmid = {41091222}, issn = {1432-1831}, support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; }, mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.}, } @article {pmid40915146, year = {2025}, author = {Leonard, SR and Mammel, MK and Brassill, N and Champ, C and Lacher, DW and Saber, B and Kase, JA and Kataoka, A and Bell, RL and Brown, EW and Rock, CM and Musser, SM}, title = {Air microbiomes reveal presence of Shiga toxin-producing Escherichia coli in airborne cattle pen soil adjacent to large feedlot.}, journal = {The Science of the total environment}, volume = {1000}, number = {}, pages = {180375}, doi = {10.1016/j.scitotenv.2025.180375}, pmid = {40915146}, issn = {1879-1026}, mesh = {Animals ; Cattle ; *Shiga-Toxigenic Escherichia coli/isolation & purification ; *Air Microbiology ; *Soil Microbiology ; *Microbiota ; *Environmental Monitoring ; Animal Husbandry ; }, abstract = {Cattle are a reservoir for the zoonotic human foodborne pathogen Shiga toxin-producing Escherichia coli (STEC), the causative agent of many disease outbreaks associated with contaminated fresh leafy greens. Concentrated animal feeding operations (CAFOs) housing cattle generate fugitive dust, however the potential risk of STEC movement by means of the aerosolized dust is not well known. In this investigation, we used metagenome sequencing of air samples collected in an agricultural setting to investigate airborne transfer of STEC from a large CAFO to the surrounding area. Shiga toxin genes and other E. coli virulence genes were observed in air metagenomes, and their presence was positively correlated with abundance of cattle mitochondrial DNA (mtDNA). Air bacterial community composition differed based on STEC presence, and source tracking utilizing the air metagenomes indicated that cattle feedlot soil contributed to the air bacterial communities. Moreover, a novel biomarker for cattle pen soil, Corynebacterium maris, was identified that correlated with both E. coli virulence gene presence and cattle mtDNA abundance. Overall, our results demonstrate a definitive link between aerosolized cattle feedlot dust and airborne STEC transfer to adjacent and nearby agricultural fields. This work highlights the importance of including the potential for airborne transmission of pathogens in risk assessments for contamination by human foodborne pathogens of fresh produce grown in proximity to CAFOs.}, } @article {pmid40812705, year = {2025}, author = {Gao, H and Guo, Z and Huang, F and Li, S and He, X and Fernio, JU and Lv, W and Zhou, L and Du, S and Shen, M and Xu, R}, title = {Core microbiota with antimonite oxidation coupled nitrogen fixation traits persist in the rhizosphere of pioneer plants in antimony tailings.}, journal = {Environmental research}, volume = {285}, number = {Pt 4}, pages = {122586}, doi = {10.1016/j.envres.2025.122586}, pmid = {40812705}, issn = {1096-0953}, mesh = {*Antimony/metabolism ; *Rhizosphere ; *Nitrogen Fixation ; *Microbiota ; Oxidation-Reduction ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Poaceae/microbiology ; Mining ; Bacteria ; }, abstract = {Antimony (Sb) tailings pose a dual challenge to plant colonization, combining high metal(loid) toxicity with nitrogen (N) limitation, both of which constrain pioneer plant establishment and hinder ecological restoration. Rhizosphere microbiota, particularly Sb(III) oxidation coupled with nitrogen fixation (SbNF) taxa, are critical in mitigating such stresses. However, the composition and persistence of these functional microbes may vary across plant species, leading to untargeted selection. Here, we investigated the rhizosphere microbiomes of two pioneer species-Miscanthus sinensis (herbaceous) and Boehmeria nivea (shrubby)-in Sb tailings. A shared core microbiota (>20 % of the genera) was identified, within which certain taxa exhibited SbNF capabilities with plant growth-promoting (PGP) potential. Through integrated metagenomic binning, culture-based isolation, and functional validation, we identified core genera, such as Pseudomonas and Streptomyces, that were consistently enriched across plant types and exhibited robust SbNF capacities, versatile PGP traits, and community assembly interactions. These findings reveal a conserved assembly mechanism of functional rhizobacteria in Sb-stressed environments and offer promising microbial candidates for the development of bioinoculants to support phytoremediation in metalloid-contaminated ecosystems.}, } @article {pmid40455595, year = {2025}, author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL}, title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.}, journal = {Integrative and comparative biology}, volume = {65}, number = {4}, pages = {942-954}, doi = {10.1093/icb/icaf073}, pmid = {40455595}, issn = {1557-7023}, support = {KA2017-91786//Charles E. Kaufman Foundation/ ; //Kenneth P. Dietrich School of Arts and Sciences/ ; }, mesh = {*Pollination ; *Pollen/virology ; *Plant Viruses/physiology ; *Biodiversity ; Animals ; *Magnoliopsida/virology/physiology ; Flowers/virology ; }, abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether (1) life history, floral traits, or pollination generalism were associated with viral richness, and (2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.}, } @article {pmid41089454, year = {2025}, author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G}, title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1666201}, pmid = {41089454}, issn = {1664-302X}, abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.

METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.

RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.

DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.}, } @article {pmid41088378, year = {2025}, author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y}, title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1097}, pmid = {41088378}, issn = {1479-5876}, support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; }, abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.}, } @article {pmid41088296, year = {2025}, author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J}, title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1083}, pmid = {41088296}, issn = {1479-5876}, support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adolescent ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Male ; Female ; *Emotions ; Quetiapine Fumarate/therapeutic use/pharmacology ; Magnetic Resonance Imaging ; Case-Control Studies ; Brain/physiopathology/diagnostic imaging ; Neuroimaging ; }, abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.

METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.

RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC = 91.12%) and predict the treatment effect (AUC = 91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.

CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .}, } @article {pmid41087898, year = {2025}, author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C}, title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {660}, pmid = {41087898}, issn = {1471-2180}, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/blood/metabolism ; *Mycobiome ; *Gastrointestinal Microbiome ; *Metabolome ; Male ; Female ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Feces/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; }, abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.

METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.

RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.

CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.}, } @article {pmid41087864, year = {2025}, author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X}, title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {663}, pmid = {41087864}, issn = {1471-2180}, support = {82100594//National Natural Science Foundation of China,China/ ; }, mesh = {Animals ; *Helicobacter Infections/microbiology/metabolism/complications ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Helicobacter pylori/physiology ; Mice ; Humans ; Mice, Inbred C57BL ; *Homeostasis ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; Male ; Retrospective Studies ; *Glucose/metabolism ; Glucagon-Like Peptide 1/metabolism ; Female ; Middle Aged ; Colon/microbiology/metabolism ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents ; Insulin Resistance ; Diabetes Mellitus, Experimental/microbiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.

METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.

RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.

CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).}, } @article {pmid41087370, year = {2025}, author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D}, title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35782}, pmid = {41087370}, issn = {2045-2322}, mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; }, abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.}, } @article {pmid41043233, year = {2025}, author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F}, title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.}, journal = {Ecotoxicology and environmental safety}, volume = {304}, number = {}, pages = {119145}, doi = {10.1016/j.ecoenv.2025.119145}, pmid = {41043233}, issn = {1090-2414}, mesh = {Animals ; Swine ; Oxidative Stress/drug effects ; Apoptosis/drug effects ; Enterotoxigenic Escherichia coli/physiology ; Gastrointestinal Microbiome/drug effects ; Liver/drug effects ; *Metabolome/drug effects ; *Metagenome/drug effects ; *Escherichia coli Infections/veterinary/drug therapy ; Inflammation ; Weaning ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.}, } @article {pmid41015306, year = {2026}, author = {Hou, DJ and Guo, WL and Yang, HW and Liu, QR and Fan, NS and Jin, RC}, title = {Behaviors and adaptive strategies of anammox microbiota in response to typical ionic liquid: Metabolic compensation and gene regulation.}, journal = {Bioresource technology}, volume = {439}, number = {}, pages = {133395}, doi = {10.1016/j.biortech.2025.133395}, pmid = {41015306}, issn = {1873-2976}, mesh = {*Ionic Liquids/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonium Compounds/metabolism ; Wastewater/microbiology ; Oxidation-Reduction ; Anaerobiosis ; *Gene Expression Regulation, Bacterial/drug effects ; Bacteria/metabolism/genetics/drug effects ; Molecular Docking Simulation ; }, abstract = {Ionic liquids (ILs) have been used to replace organic solvents, thereby causing challenges for wastewater treatment. Anaerobic ammonium oxidation (anammox) had been recognized to treat high-strength ammonium wastewater, but its response to ILs remains unclear. Metagenomic sequencing, granule characterization and molecular docking simulation were employed to investigate the comprehensive effects of 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) on anammox consortia. [EMIM][Ac] of 2 mg L[-1] reduced the specific anammox activity (SAA) by 46.0 %. [EMIM][Ac] also induced oxidative stress. The higher abundance of denitrifying bacteria and functional genes (nirK and nirS) compensated for the reduced nitrogen removal efficiency. In P2, the total abundance of nirK and nirS in R1 was 16.2 % higher than its initial value, and also 9.6 % higher than that in R0. This study elucidated how anammox microbiota resisted ILs via metabolic regulation and EPS secretion, providing a theoretical support for improving the feasibility and efficiency of anammox-based wastewater treatment systems.}, } @article {pmid40914221, year = {2025}, author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y}, title = {Succession-driven potential functional shifts in microbial communities in the tire-plastisphere: Comparison of pristine and scrap tire.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {385}, number = {}, pages = {127074}, doi = {10.1016/j.envpol.2025.127074}, pmid = {40914221}, issn = {1873-6424}, mesh = {*Microbiota ; *Microplastics/analysis ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Bacteria ; Lakes/microbiology ; }, abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.}, } @article {pmid40896895, year = {2025}, author = {Jiang, Z and Yang, S and Pang, Q and Abdalla, M and Karbin, S and Qi, S and Hu, J and Qiu, H and Song, X and Smith, P}, title = {Metagenomic insights into the influence of soil microbiome on greenhouse gas emissions from paddy fields under varying irrigation and fertilisation regimes.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127129}, doi = {10.1016/j.jenvman.2025.127129}, pmid = {40896895}, issn = {1095-8630}, mesh = {*Greenhouse Gases ; Fertilizers ; *Agricultural Irrigation ; *Soil Microbiology ; Soil/chemistry ; *Microbiota ; China ; Agriculture ; Oryza ; Methane ; }, abstract = {Integration of diverse fertilisation strategies with water-saving irrigation techniques presents a promising sustainable agricultural practice, offering the potential to reduce greenhouse gases (GHGs) emissions, enhance carbon sequestration and boost crop yields. However, existing research on the influence of soil microorganisms on biogeochemical processes of GHGs is limited. Herein, we explored the microbial mechanisms influencing GHGs emissions through a 3-year field experiment and metagenomic sequencing conducted in southeastern China. We investigated two irrigation patterns (controlled irrigation [CI] and flooded irrigation [FI]) and three fertilisation strategies (chemical fertiliser [F], straw returning [S] and manure substitution [M]). Results indicated that irrigation patterns significantly affected the microbial community structure in paddy soil. The key environmental factors affecting microorganisms at the phylum level included soil pH, moisture content, total nitrogen content and CH4 emissions. Random forest analysis further identified Cyanobacteria, Nitrospirae, Kiritimatiellaeota, Proteobacteria, and Balneolaeota as dominant phyla driving the differences in microbial communities across treatments. Under CI, an increase in N2O emissions was observed, which was driven by key genes, such as nirS, nirK, nosZ and norB. Compared with CF (CI with F), S increased the abundance of nirS and nirK, leading to higher N2O emissions, whereas M increased the abundance of nosZ, thereby reducing N2O emissions. The genes mcrA, pmoA and pmoC were responsible for elevated CH4 emissions through straw incorporation and manure application. Structural equation model analysis revealed that the irrigation pattern significantly affected CH4 emissions and rice yield, while the fertilisation type mainly influenced soil pH and rice yield. Organic input, particularly manure, resulted in higher C emissions owing to the presence of more CH4-producing gene mcrA in the soil. Overall, the combination of CI and manure is recommended for reducing GHGs emissions, enhancing C sequestration and boosting rice yields.}, } @article {pmid40882272, year = {2025}, author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M}, title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127108}, doi = {10.1016/j.jenvman.2025.127108}, pmid = {40882272}, issn = {1095-8630}, mesh = {*Denitrification ; *Wastewater/chemistry ; *Microalgae/metabolism ; Carbon ; Nitrates ; Bacteria/metabolism ; Nitrogen ; Microbial Consortia ; }, abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.}, } @article {pmid40882267, year = {2025}, author = {Davis, BC and Linz, D and McMinn, BR and Korajkic, A}, title = {Limited ARG removal but stable resistome dynamics in a surface flow constructed wetland.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {126986}, doi = {10.1016/j.jenvman.2025.126986}, pmid = {40882267}, issn = {1095-8630}, mesh = {*Wetlands ; Wastewater/microbiology ; Bacteria/genetics ; Microbiota ; Anti-Bacterial Agents ; }, abstract = {Improperly treated wastewater and surface runoff can degrade water quality by introducing microbial contaminants, including antibiotic-resistant bacteria (ARB) and their genes (ARGs). Constructed treatment wetlands (CTWs) offer a low-resource solution for managing impaired watersheds. However, their ability to mitigate microbial contaminants, particularly ARGs, requires further study. In this study, 62 water samples from Banklick Creek CTW (BCTW) were shotgun sequenced to assess ARG dynamics and removal characteristics. Results showed minimal resistome attenuation, likely due to the wetland's horizontal surface flow design with short, variable hydraulic residence times (0.48-3.1 days). Despite this, 198 low-abundance ARGs were removed, accounting for a median of 0.52 % (0-3.1 %) of total ARG abundance upstream. The core resistome, comprising 95.6 ± 1.9 % of total ARG abundance, was stable and mainly consisted of multidrug efflux systems carried by bacterioplankton and macrophyte symbionts, indicating a native resistome reflective of regional pollution history. Resistome and microbiome structures were highly correlated (R[2] = 0.808), with ARGs rarely co-occurring with mobile genetic elements, indicating limited intercellular transfer potential. No significant correlations were found between resistome dynamics and human fecal (HF183, crAssphage) or avian (GFD) biomarkers. Although several class-one integron-integrase (intI1) contigs were enriched in treatment channels, gene cassette cargo was void of ARGs. As detection of intI1 via qPCR is generally considered indicative of resistome mobility potential, this finding carries important implication for intI1 qPCR assay selection (i.e., targeting clinical intI1 mosaics) and over-interpretation of ARG spread in the environment.}, } @article {pmid40834570, year = {2025}, author = {Ansari, SA and Ramteke, A and Sawarkar, R and Kumar, T and Khan, D and Agashe, A and Patil, MP and Singh, L}, title = {"Innovative approaches in microbial community engineering for food waste management: A comprehensive review".}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {127000}, doi = {10.1016/j.jenvman.2025.127000}, pmid = {40834570}, issn = {1095-8630}, mesh = {*Waste Management/methods ; Biodegradation, Environmental ; *Microbial Consortia ; Metabolic Engineering ; Fermentation ; }, abstract = {Food waste (FW) is a critical global issue, exacerbating environmental degradation and resource scarcity. Traditional FW management methods are often inefficient and unsustainable. This review highlights advances in microbial community engineering for FW valorization, focusing on synthetic biology, metagenomics, metabolic engineering, and electro-fermentation. Engineered microbial consortia enhance the breakdown of complex organics while producing bioenergy, bioplastics, and organic acids. Metagenomics enables precise metabolic optimizations, and electro-fermentation improves bioconversion yields. These systems outperform conventional methods in reducing greenhouse gases, recovering nutrients, and promoting a circular bioeconomy. Challenges persist, including microbial stability, scalability, and incomplete knowledge of interspecies interactions. Future research should integrate AI and machine learning to design robust synthetic consortia and optimize metabolic pathways. Scaling electrochemical technologies (e.g., microbial electrosynthesis) requires further validation. Standardized biosafety protocols, techno-economic analyses, and supportive policies are essential for industrial adoption. Interdisciplinary collaboration is crucial to address these gaps. In conclusion, microbial engineering offers a sustainable FW management solution, improving biodegradation efficiency and resource recovery. Future efforts must prioritize scalable, stable systems with real-time monitoring and ecological safety. Overcoming these challenges will enable engineered microbes to mitigate environmental impacts, generate renewable energy, and advance a resource-efficient future.}, } @article {pmid40796326, year = {2025}, author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS}, title = {Alterations of the Upper Respiratory Microbiome Among Children Living With HIV Infection in Botswana.}, journal = {The Journal of infectious diseases}, volume = {232}, number = {4}, pages = {815-825}, doi = {10.1093/infdis/jiaf429}, pmid = {40796326}, issn = {1537-6613}, support = {T32 HL 007538//Institutional Training Grant in Pulmonary and Critical Care Medicine/ ; D43 TW009337/TW/FIC NIH HHS/United States ; K23-HL166022//NIH Career Development Award/ ; //Duke University Center for AIDS Research/ ; 5P30-AI064518//NIH-funded program/ ; K23-AI135090//NIH-funded program/ ; //NIH/ ; P30-AI045008//Penn Center for AIDS Research/ ; }, mesh = {Humans ; *HIV Infections/microbiology/complications ; Botswana/epidemiology ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; *Nasopharynx/microbiology ; Child, Preschool ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; }, abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory microbiome is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of Batswana children. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected and HIV-unexposed, uninfected children in a cross-sectional study. We used shotgun metagenomic sequencing to compare nasopharyngeal microbiomes by HIV status. Among the 143 children in this study, HIV and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with resistance to bacterial pathogen colonization. These findings suggest that the upper respiratory microbiome may contribute to the high risk of respiratory infections among CLWH.}, } @article {pmid40795737, year = {2025}, author = {Zhao, J and Kou, X and Liu, H and Wu, T and Li, J and Wang, Y and Xie, H and Wang, M and Wu, L and Wen, L and Wang, L}, title = {Microbial community responses and functional shifts in carbon degradation driven by water-salt gradients in lakeshore wetlands of semi-arid lakes.}, journal = {Journal of environmental management}, volume = {393}, number = {}, pages = {126893}, doi = {10.1016/j.jenvman.2025.126893}, pmid = {40795737}, issn = {1095-8630}, mesh = {*Wetlands ; *Lakes ; *Carbon/metabolism ; Soil/chemistry ; Salinity ; Soil Microbiology ; Microbiota ; Ecosystem ; }, abstract = {Wetlands, especially lakeshore ecosystems, play an essential role in global carbon (C) cycling and are strongly influenced by dynamic water-salt gradients. However, the mechanisms by which these gradients shape microbial communities and affect soil organic C (SOC) degradation remain incompletely understood. Here, we aimed to elucidate microbial mechanisms driving C degradation shifts along water-salt gradients. We investigated microbially mediated SOC degradation potential in Daihai Lake wetlands by metagenomic profiling of carbohydrate-active enzyme (CAZyme) genes. Our results demonstrated a significant shift in CAZyme gene abundances across the gradients. Genes involved in plant-derived C (cellulose, hemicellulose, lignin) degradation decreased with increasing soil salinity and moisture, while those related to microbial-derived C (chitin, peptidoglycan, glucans) decomposition were significantly enriched. Concurrently, the microbial community composition shifted toward greater abundance of salt-tolerant taxa, notably Proteobacteria and Bacteroidetes, while Actinobacteria and Firmicutes declined under higher water-salt conditions. Statistical analyses revealed strong correlations between key environmental factors (soil salinity (EC), soil moisture (SM), and pH) and both microbial community structure and CAZyme gene abundances (p < 0.001). Random Forest analysis further identified EC and SM as primary factors influencing C-degrading microbial functions. This study highlights the importance of water-salt gradients in regulating microbial-mediated C cycling in wetlands, providing critical insights into microbial adaptation strategies and their implications for wetland C dynamics under environmental change.}, } @article {pmid40581627, year = {2025}, author = {Nørgaard, JC and Marandi, RZ and Ilett, EE and Gulay, A and Paredes, R and Lundgren, JD and Jørgensen, M and Sengeløv, H}, title = {The Gut Microbiome and Its Resistome as Predictors of Clinical Infections and Phenotypic Antibiotic Resistance in Hematopoietic Stem Cell Transplant Recipients.}, journal = {The Journal of infectious diseases}, volume = {232}, number = {4}, pages = {806-814}, doi = {10.1093/infdis/jiaf330}, pmid = {40581627}, issn = {1537-6613}, support = {DNRF126//Danish National Research Foundation/ ; R167-A108665-17-S2//Danish Cancer Society/ ; R218-2016-1482//Lundbeck Foundation/ ; NNF15OC0014158//Novo Nordisk Foundation/ ; //Svend Anderson Foundation/ ; RD16/0025/0041//RED de SIDA/ ; //European Regional Development Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/drug effects/isolation & purification ; Enterococcus faecalis/drug effects/isolation & purification ; Metagenomics ; *Drug Resistance, Bacterial ; Young Adult ; Escherichia coli/drug effects/isolation & purification ; Aged ; Gram-Positive Bacterial Infections/microbiology ; Transplant Recipients ; }, abstract = {A relationship among the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here by using 663 shotgun-sequenced fecal samples from 276 stem cell transplants. Enterococcus faecium, Escherichia coli, and Enterococcus faecalis were the 3 most prevalent causes of clinical infection, with vancomycin resistance in E faecium as the most common antibiotic resistance feature. Associations among the gut microbiome, resistome, and clinical infections were tested, with significant findings (false discovery rate <0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E faecium was positively associated with subsequent clinical infection with E faecium (odds ratio, 1.14; P = .02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E faecium infection (odds ratio, 1.27; P < .01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.}, } @article {pmid40468098, year = {2025}, author = {Srivastava, A and Rai, PK and Agnihotri, VK and Choure, K and Vishvakarma, R}, title = {Metagenomic analysis of viral communities in the polluted Varuna River reveals site-specific diversity patterns associated with environmental aspects.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {7}, pages = {2129-2150}, pmid = {40468098}, issn = {1618-1905}, mesh = {*Rivers/virology ; Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Phylogeny ; *Virome ; }, abstract = {Varuna River, which is native to Varanasi, is of great importance as a water reservoir for the people and is contaminated with heavy pollutants due to urbanization. In this study, four sites (VR1, VR2, VR3, and VR4) of Varuna River water were sampled to assess the viral diversity. The metagenomics approach was used to study the viral diversity and functional analysis, suggesting the overall quality of the water at the sampled location. The analysis shows that VR1 had the most species richness (3000 species), followed by VR3 (2500), VR2 (2000), and VR4 (1500). The PCA analysis revealed distinct spatial patterns and community differentiation where VR2 and VR4 clustered while VR1 and VR3 were distant.Diversity analysis showed that Negarnaviricota dominated all samples at the phylum level. Yunchangviricetes, a non-reported virus, and Insthoviricetes were the dominant classes. Pakpunavirus was the leading genus, followed by the human pathogen Mimivirus. The highest species abundance in VR1 and VR2 was Mimivirus, Megavirus, chilensis, while VR3 and VR4 had Hpunavirus and Pseudomonas phage O4, indicating human involvement. Functional analyses of enzymatic activity and KEGG Orthology in microbial communities from VR1 to VR4 samples showed that VR4 exhibited maximal enzymatic activity, genetic flexibility, and advanced regulatory control compared to the other samples. The increased presence of transporter genes alongside signal transduction proteins and metabolic enzymes in VR4 indicates enhanced functional diversity, which aids in coping with environmental stresses. On the basis of viral species, ecological, biotechnological aspects were also interpreted. This study concluded that the Negarnaviricota plays a key role in maintaining the overall water quality and there is an urgent need for remediation of the Varuna River especially at site VR4 (25° 19' 46.7″ N 83° 02' 38.3″ E).}, } @article {pmid40439813, year = {2025}, author = {Biktasheva, L and Galitskaya, P and Kuryntseva, P and Shipaeva, M and Selivanovskaya, S}, title = {Challenges and distortions in microbial community analysis of oil reservoirs: a case study with heavy crude oil from the Romashkino field.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {7}, pages = {2095-2103}, pmid = {40439813}, issn = {1618-1905}, support = {075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Oil and Gas Fields/microbiology ; *Petroleum/microbiology/analysis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; DNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; }, abstract = {The study of the microbial community of wells is a methodologically complex, but urgent problem. In the course of our work, five samples of oil wells were selected from one deposit of the Romashkino field. The samples were subjected to nucleic acid extraction using three methods-direct DNA extraction, and after enrichment using aerobic and anaerobic cultivation methods. In three samples from wells W1-W3, extraction after anaerobic enrichment was successful. Effective aerobic cultivation was possible in all five samples. All three of these samples represented the aqueous part of the produced fluid; samples from wells W4 and W5, where extraction was difficult, represented the oil part. During the analysis of the microbial community in enrichment cultures from wells W1-W3, exogenous microorganisms such as Desulfovibrio, Acetobacterium, Bacillus, and Georgenia were discovered, which can be explained by the long-term exploitation of this section of the field. In one sample from well W1, community information was obtained using direct extraction and anaerobic enrichment. It was found that the microbial community changed significantly after enrichment, and its diversity decreased. At the same time, however, the functional profile of microorganisms has not changed, and sulfate-reducing microorganisms dominate in both samples. Thus, the results of the work allow us to make an assumption about the physicochemical parameters of samples in which the study of the microbial community is possible. In addition, it became known that well W1 needs to control the process of biological acidification and has a high risk of equipment corrosion.}, } @article {pmid40411710, year = {2025}, author = {Chen, L and Chen, C and Bai, Y and Li, C and Wei, C and Wei, R and Luo, R and Li, R and Ma, Q and Geng, Y}, title = {Evaluation of the effects of different formulations of protectants on the preservation of the microbiota in fecal microbiota transplantation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {7}, pages = {2057-2079}, pmid = {40411710}, issn = {1618-1905}, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Bacteria/drug effects/genetics/growth & development ; *Protective Agents/pharmacology/chemistry ; Microbial Viability/drug effects ; *Preservation, Biological/methods ; Freeze Drying ; Male ; }, abstract = {BACKGROUND: With the increasing indications for fecal microbiota transplantation for the treatment of diseases, there is a growing demand for the preparation of frozen or lyophilized fecal microbiota products that are viable and can stably colonize the recipient. The addition of protective agents plays an important role in the preparation. However, there has been no systematic evaluation of the protective agents used in fecal microbiota sample transplantation preparation for transplantation.

METHODS: We were used the donor bacterial flora containing 10 different formulations of protective agents were frozen, lyophilized, and stored. Plate counting, CCK8 assay, flow cytometry after LIVE/DEAD staining, and fluorescence intensity were used to assess viable bacteria in vitro. In addition, the donor bacterial flora samples containing different formulations protective agents were transplanted into antibiotic-treated SPF mice, with 3 mice in each group and a total of 5 groups. Fecal samples were collected for metagenomic sequencing to observe the colonization of the bacterial flora in the recipient mice.

RESULTS: The preliminary screening results showed that the survival rate of bacteria in the 5% trehalose (T) groups, and 5% sucrose, 5% inulin, and 1% cysteine hydrochloride (SI) groups was slightly higher than that in the other groups. SI groups tended to be more protective against anaerobes than T groups. The donor gut microbiota containing the SI groups protective agent exhibited the best colonization of the recipient mice. The protective effects of different formulations of protective agents on the colonized probiotic strains and the metabolic function of the bacterial flora in recipient mice were found to be species specific.

CONCLUSIONS: SI groups can not only better protect the activity of anaerobic bacteria in the intestine, but also effectively promote the effective colonization of donor intestinal bacteria in the recipient mice, and the effect of frozen storage method is less, and can be used at the same time as frozen and freeze-dried preparation. It can be used as a reference for the selection of protective agents in the preparation of fecal microbiota transplantation samples.}, } @article {pmid40402820, year = {2025}, author = {Alberdi, A and Limborg, MT and Groussin, M and Aizpurua, O and Gilbert, MTP}, title = {Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {10}, pages = {1285-1298}, doi = {10.1093/jeb/voaf063}, pmid = {40402820}, issn = {1420-9101}, support = {DNRF143//Danish National Research Foundation/ ; R250-2017-1351//Lundbeckfonden/ ; CF20-0460//Carlsbergfondet/ ; H2020-SFS-2018-1//European Union/ ; HoloFood-817729//European Union/ ; 901436//Norwegian Seafood Research Fund/ ; 1182//German Science Foundation/ ; 261376515-SFB 1182//German Science Foundation/ ; }, mesh = {Animals ; *Biological Evolution ; *Microbiota ; *Metagenomics ; *Vertebrates/microbiology ; Host Microbial Interactions ; }, abstract = {Microorganisms are essential for the normal functioning of most vertebrates. Hence, identifying and measuring the factors that shape host-associated microbial communities is necessary to understand the ecological and evolutionary implications of host-microbiota associations. We propose a framework, built on the so-called "metagenomic space" concept, which incorporates multiple definitions and quantifiable features relating to the variation of microbial communities that are associated with vertebrate hosts. By drawing on diverse theories and concepts developed in different fields of biology, our framework sets a conceptual landscape that transcends the mere characterization of microbial communities. This provides the basis to study more complex attributes, such as "potential metagenomic space" and "fundamental metagenomic space," "metagenomic plasticity," and "metagenomic evolvability," which we argue are essential for understanding the microbial contribution to vertebrate host ecology and evolution-and hold considerable promise for advancing applied research and innovation. In doing so, we hope to contribute to an improved understanding of the impact of spatiotemporal variation of vertebrate host-microbiota associations, and inspire new approaches to address testable hypotheses related to ecological, evolutionary, and applied processes.}, } @article {pmid40266232, year = {2025}, author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y}, title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf076}, pmid = {40266232}, issn = {1751-7370}, support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; //Shandong Provincial Key Research and Development Program of China/ ; //National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Chickens/microbiology/immunology ; *Gastrointestinal Microbiome ; *Homeostasis ; *Intestines/microbiology/immunology ; *Bacteria/genetics/classification ; *Salmonella Infections, Animal/immunology/prevention & control/microbiology ; Phylogeny ; Poultry Diseases/immunology/microbiology ; *Salmonella/immunology ; }, abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a 10-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early-life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria (SFB), which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of SFB from the chicken gut microbiota, which displayed common metabolic deficiencies with SFB of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of SFB in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.}, } @article {pmid40134271, year = {2025}, author = {Orme, W and Grimm, SL and Vella, DSN and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Coarfa, C and Madan, A}, title = {Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients.}, journal = {The Journal of neuropsychiatry and clinical neurosciences}, volume = {37}, number = {4}, pages = {349-358}, doi = {10.1176/appi.neuropsych.20240126}, pmid = {40134271}, issn = {1545-7222}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Inpatients ; *Personality/physiology ; *Mental Disorders/microbiology ; Machine Learning ; Feces/microbiology ; Young Adult ; *Personality Disorders/microbiology ; }, abstract = {OBJECTIVE: Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.

METHODS: In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.

RESULTS: Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R[2]>0.20), perceptual disturbance (maximum AUROC=0.763, R[2]=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.

CONCLUSIONS: Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.}, } @article {pmid41085703, year = {2025}, author = {Sharma, N and Verma, A and Ambardar, S and Raj, S and Vakhlu, J}, title = {Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.}, journal = {Molecular genetics and genomics : MGG}, volume = {300}, number = {1}, pages = {97}, pmid = {41085703}, issn = {1617-4623}, support = {Rashtriya Uchchatar Shiksha Abhiyan//Rashtriya Uchchatar Shiksha Abhiyan/ ; JKST&IC/J/14/2022/160//JKST&IC-JKDST/ ; DST-INSPIRE/03/2022/004594//DST-INSPIRE/ ; BT/AIR01624/PACE-28/22//BIRAC-PACE/ ; }, mesh = {*Crocus/microbiology/genetics ; *Software ; *Metagenome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Algorithms ; }, abstract = {Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.}, } @article {pmid41084448, year = {2025}, author = {Han, Z and Jin, LX and Wang, ZT and Yang, LQ and Li, L and Ruan, Y and Chen, QW and Yao, SH and Heng, XP}, title = {[Regulatory effects of Dangua Humai Oral Liquid on gut microbiota and mucosal barrier in mice with glucolipid metabolism disorder].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {50}, number = {15}, pages = {4315-4324}, doi = {10.19540/j.cnki.cjcmm.20250421.401}, pmid = {41084448}, issn = {1001-5302}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/administration & dosage ; Mice, Inbred C57BL ; Humans ; *Glycolipids/metabolism ; Lipid Metabolism/drug effects ; Administration, Oral ; Disease Models, Animal ; }, abstract = {The gut microbiota regulates intestinal nutrient absorption, participates in modulating host glucolipid metabolism, and contributes to ameliorating glucolipid metabolism disorder. Dysbiosis of the gut microbiota can compromise the integrity of the intestinal mucosal barrier, induce inflammatory responses, and exacerbate insulin resistance and abnormal lipid metabolism in the host. Dangua Humai Oral Liquid, a hospital-developed formulation for regulating glucolipid metabolism, has been granted a national invention patent and demonstrates significant clinical efficacy. This study aimed to investigate the effects of Dangua Humai Oral Liquid on gut microbiota and the intestinal mucosal barrier in a mouse model with glucolipid metabolism disorder. A glucolipid metabolism disorder model was established by feeding mice a high-glucose and high-fat diet. The mice were divided into a normal group, a model group, and a treatment group, with eight mice in each group. The treatment group received a daily gavage of Dangua Humai Oral Liquid(20 g·kg~(-1)), while the normal group and model group were given an equivalent volume of sterile water. After 15 weeks of intervention, glucolipid metabolism, intestinal mucosal barrier function, and inflammatory responses were evaluated. Metagenomics and untargeted metabolomics were employed to analyze changes in gut microbiota and associated metabolic pathways. Significant differences were observed between the indicators of the normal group and the model group. Compared with the model group, the treatment group exhibited marked improvements in glucolipid metabolism disorder, alleviated pathological damage in the liver and small intestine tissue, elevated expression of recombinant claudin 1(CLDN1), occluding(OCLN), and zonula occludens 1(ZO-1) in the small intestine tissue, and reduced serum levels of inflammatory factors lipopolysaccharides(LPS), lipopolysaccharide-binding protein(LBP), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α). At the phylum level, the relative abundance of Bacteroidota decreased, while that of Firmicutes increased. Lipid-related metabolic pathways were significantly altered. In conclusion, based on the successful establishment of the mouse model of glucolipid metabolism disorder, this study confirmed that Dangua Humai Oral Liquid effectively modulates gut microbiota and mucosal barrier function, reduces serum inflammatory factor levels, and regulates lipid-related metabolic pathways, thereby ameliorating glucolipid metabolism disorder.}, } @article {pmid41083440, year = {2025}, author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P}, title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9069}, pmid = {41083440}, issn = {2041-1723}, support = {225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; }, abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.}, } @article {pmid41032855, year = {2025}, author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M}, title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.}, journal = {Environmental science & technology}, volume = {59}, number = {40}, pages = {21540-21554}, doi = {10.1021/acs.est.5c01564}, pmid = {41032855}, issn = {1520-5851}, mesh = {*Wetlands ; *Microbiota ; Archaea ; Bacteria ; China ; Ecosystem ; Metagenome ; }, abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.}, } @article {pmid40726432, year = {2025}, author = {Hua, R and Ding, N and Hua, Y and Wang, X and Xu, Y and Qiao, X and Shi, X and Bai, T and Xiong, Y and Zhuo, X and Fan, C and Zhou, J and Wu, Y and Liu, J and Yuan, Z and Li, T}, title = {Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {38}, pages = {e01707}, doi = {10.1002/advs.202501707}, pmid = {40726432}, issn = {2198-3844}, support = {2021YFA1301201//National Key R&D Program of China/ ; 2021YFA0805400//National Key R&D Program of China/ ; 2024YFA1307004//National Key R&D Program of China/ ; 82000474//National Science Foundation of China/ ; 82370458//National Science Foundation of China/ ; 82370875//National Science Foundation of China/ ; 82430019//National Science Foundation of China/ ; 2021KJXX-04//Innovative Talents Promotion Plan of Shaanxi Province of China/ ; xzy012019093//Xi'an Jiaotong University/ ; 2020JM-383//Natural Science Foundation of Shaanxi Province/ ; }, mesh = {*Atherosclerosis/metabolism/microbiology ; Animals ; Mice ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Pyroptosis/drug effects/physiology ; Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; *Macrophages/metabolism ; Probiotics/pharmacology ; Humans ; *Lactobacillus johnsonii/metabolism ; Mice, Inbred C57BL ; *Lactobacillus/metabolism ; Male ; Disease Models, Animal ; }, abstract = {Gut microbiota and their metabolites are remarkable regulators in atherosclerosis. Oral drugs such as aspirin have recently been found to modulate the gut microbiome. However, the roles of drug-microbiota-metabolite interactions in atherosclerosis have not been explored. Herein, two gut probiotics, Ligilactobacillus murinus (L. murinus) and Lactobacillus johnsonii (L. johnsonii), are identified from mouse models and human cohorts, which are positively correlated with aspirin usage. Specifically, the eradication of these two species eliminated aspirin's anti-atherosclerotic effects, while their transplantation exhibited therapeutic effects against atherosclerosis. Integrative analysis of metagenomic and metabolomic data showed that elevated levels of butyrate are associated with these two species. Mechanically, L. murinus and L. johnsonii form symbiotic networks with butyrate-producing bacteria such as Allobaculum. This study confirmed that gut microbes produce butyrate, which helps preserve the gut barrier and prevents the leakage of lipopolysaccharides. By integrating molecular biology and single-cell sequencing data, G protein-coupled receptor 109A (GPR109A) is confirmed as the direct target of butyrate. Through the activation of GPR109A, butyrate produced by L. murinus and L. johnsonii suppressed the expression of Gasdermin D (GSDMD) in the pyroptosis of macrophages during atherosclerosis. These findings offer novel insights into the drug-microbiota axis that can be targeted to improve the treatment of atherosclerosis.}, } @article {pmid41082055, year = {2025}, author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA}, title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {10}, pages = {377}, pmid = {41082055}, issn = {1573-0972}, mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.}, } @article {pmid41080577, year = {2025}, author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z}, title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1636876}, pmid = {41080577}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; }, abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.}, } @article {pmid41077635, year = {2025}, author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , }, title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.}, journal = {Comprehensive Physiology}, volume = {15}, number = {5}, pages = {e70058}, doi = {10.1002/cph4.70058}, pmid = {41077635}, issn = {2040-4603}, support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.

METHODS: We performed metagenomic whole genome sequencing (mWGS; > 25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.

RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p = 0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p = 0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p = 0.05) but reduced compared to healthy individuals (0.20; p < 0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p = 0.06) and healthy (0.01; p = 0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.

CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.}, } @article {pmid41074949, year = {2025}, author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H}, title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {82}, number = {1}, pages = {354}, pmid = {41074949}, issn = {1420-9071}, support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; }, mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; }, abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.}, } @article {pmid41061488, year = {2026}, author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N}, title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.}, journal = {International journal of food microbiology}, volume = {444}, number = {}, pages = {111479}, doi = {10.1016/j.ijfoodmicro.2025.111479}, pmid = {41061488}, issn = {1879-3460}, mesh = {*Raphanus/microbiology/virology ; Fermentation ; *Bacteriophages/genetics/physiology/isolation & purification/classification ; *Bacteria/virology/genetics/classification/isolation & purification ; Food Microbiology ; Fermented Foods/microbiology/virology ; Fungi/isolation & purification/genetics/classification/virology ; Microbiota ; }, abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.}, } @article {pmid40972462, year = {2026}, author = {Wang, X and Luo, Y and Gu, Y and Ren, T and Liu, Y and Wang, X and Zhao, N and Nie, X and Liu, D and Zhao, Z}, title = {Physicochemical properties, microbial diversity, metabolites and their potential relationships of traditional Chinese Zhacai fermented for different periods.}, journal = {International journal of food microbiology}, volume = {444}, number = {}, pages = {111447}, doi = {10.1016/j.ijfoodmicro.2025.111447}, pmid = {40972462}, issn = {1879-3460}, mesh = {Fermentation ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Fungi/metabolism/classification/isolation & purification/genetics ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Amino Acids/analysis ; Biodiversity ; Hydrogen-Ion Concentration ; }, abstract = {In this study, we investigated the physicochemical properties, dominant microorganisms, non-volatile metabolites and their relationships of traditional Chinese Zhacai (TCZ) at the "second-time pickling and pressing" stage fermentation. pH and amino acid nitrogen contents exhibited an increasing and then decreasing trend. Metagenomics analysis revealed the dominant bacterial species Lactiplantibacillus (Lpb.) plantarum and Latilactobacillus (Lat.) sakei, and fungal species Debaryomyces (D.) hansenii. LEfSe analysis identified a total of 47 differentially abundant bacteria, including Lpb. plantarum and Lat. Sakei. Metabolomics analysis indicated organic acids and their derivatives, organic heterocyclic compounds, lipids and lipid-like molecules as the major differential metabolites. Spearman's correlation results showed significant correlations among differential bacteria, non-volatile metabolites and physicochemical properties. Unexpectedly, differential fungi were not observed in TCZ at this fermentation period. Pathway enrichment identified phenylpropanoid biosynthesis and tryptophan metabolism as dominant metabolic pathways, both influencing the TCZ flavor development. This study contributes to further understanding of quality formation of TCZ, providing a foundational resource for future optimization and industrial application.}, } @article {pmid40886575, year = {2025}, author = {Agga, GE and Looft, T and Sistani, KR}, title = {Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application.}, journal = {The Science of the total environment}, volume = {999}, number = {}, pages = {180306}, doi = {10.1016/j.scitotenv.2025.180306}, pmid = {40886575}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Microbiota ; Animals ; Poultry ; *Drug Resistance, Microbial/genetics ; Fertilizers ; *Manure/microbiology ; Soil/chemistry ; }, abstract = {Poultry litter (PL) is often used for soil amendment as an alternative to chemical fertilizers. However, it may enrich microbial and antimicrobial resistance genes in applied soil. The objective of this study was to investigate changes in the soil microbiome and resistome profiles following PL application. Three treatments untreated control (UC), chemical fertilizer (CF), and PL were applied to corn plots in a completely randomized block design. Total soil (metagenomic) DNA (n = 72) obtained on d0, d7, and d28 were shotgun sequenced. A composite DNA sample pooled from PL samples (n = 8) was sequenced for comparison. While Actinomycetota and Pseudomonadota were the most prevalent phyla among the soil samples, their abundance was significantly higher in the PL amended soils. PL soil amendment shifted microbial composition (Gammaproteobacteria and fungal Saccharomycetes were enriched in PL amended soils), diversity, and abundance by differentially enriching several microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. Macrolides-lincosamides-streptogramin (MLS) resistance genes were the most abundant genes enriched in PL amended soils. The PL microbiome was primarily composed of the phylum Bacillota with Virgibacillus alimentarius being the most abundant species, followed by Staphylococcus nepalensis and S. simulans. The PL resistome was dominated by MLS resistance genes. Virulence factor genes associated with the genera Bacteriodes, Enterococcus and Staphylococcus were the most prevalent. The study clearly showed that PL application enriches soil microbiome and resistome, the mechanism of which is more likely through nutrient enrichment rather than their direct transfer since PL and PL-amended soils had different microbiome profiles.}, } @article {pmid40879860, year = {2025}, author = {Liu, Y and Wang, Q and Zhang, Y and Duo, R and Bian, X and Tian, J and Hao, J and Zheng, J and Shen, H}, title = {Multi-omics characterization of gut microbiota and fecal and plasma metabolites in patients with primary Sjögren's syndrome.}, journal = {Clinical rheumatology}, volume = {44}, number = {10}, pages = {4103-4118}, pmid = {40879860}, issn = {1434-9949}, support = {CY2021-QN-A10//the Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital/ ; 2022-ZD-101//Science and Technology Program of Lanzhou city/ ; GSWSKY2023-08//Health Industry Scientific Research Project of Gansu Province/ ; }, mesh = {Humans ; *Sjogren's Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology/chemistry ; Middle Aged ; Male ; Adult ; Metabolomics ; *Metabolome ; Case-Control Studies ; Metagenomics ; Aged ; Multiomics ; }, abstract = {INTRODUCTION: Accumulating evidence has implicated gut microbiota and their metabolites in primary Sjögren's syndrome (pSS) pathogenesis. However, no study simultaneously explores the gut microbiome, microbial, and plasma metabolome in pSS patients.

METHOD: Thirty pSS patients and 60 healthy controls (HCs) were recruited. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool and plasma samples.

RESULTS: pSS patients exhibited significant reduction in microbial richness and diversity. Bacteroidetes and Firmicutes accounted for over 80% of all phyla. Four phyla, 48 genera, and 106 species with significant differences were identified (P < 0.05). Proteobacteria, Ascomycota, Fusobacteria, and 31 genera (e.g., Escherichia, Veillonella, Prevotella, Klebsiella) were enriched in pSS, while Actinobacteria, Bifidobacterium, Dorea, and Blautia were depleted. Opportunistic pathogens (e.g., Escherichia coli, Prevotella copri, Streptococcus oralis, Klebsiella pneumoniae, Enterococcus faecalis) and pathogenic Clostridium bolteae and Fusobacterium nucleatum were more abundant in pSS, whereas beneficial Bifidobacterium longum and butyrate-producing Eubacterium hallii and Anaerostipes hadrus were in HCs. Notably, Lactobacillus spp. were enriched in pSS. Of 298 differential functional pathways, 239 pSS-enriched pathways were focused on nutrient and energy metabolism, while amino acid biosynthesis in HCs. During 881 differential fecal metabolites (pSS: HCs = 631:250), fatty acyls were enriched in pSS, and glycerophospholipids in HCs. Among the 712 differential plasma metabolites (pSS: HCs = 438:274), heterocyclic compounds and benzene derivatives were more abundant in pSS, while fatty acyls and glycerophospholipids prevailed in HCs. Amino acids and organic acids were predominant in both samples.

CONCLUSIONS: This study characterized gut microbiome and fecal/plasma metabolome in pSS patients, providing theoretical support for regional pSS prevention and treatment. Key Points • This is the first study to systematically characterize the gut microbiome and fecal and plasma metabolomes of primary Sjögren's syndrome (pSS) patients in Northwest China via multi-omics integration analysis. • Significant reduction in gut microbial diversity and probiotic bacteria, enrichment of opportunistic and infectious pathogens, and microbial dysfunction were observed in pSS patients. • Much more differential fecal and plasma metabolites were observed in pSS patients, with amino acids, organic acids and derivatives, nucleotides, and metabolites being the main altered metabolites in both samples.}, } @article {pmid40202358, year = {2025}, author = {Alexandre, A and Gerard, À and Sergio, I and Wim, T and Isabelle, L and Maria José, C and Lorena, I and Enrique, H and Gerardo, MA and Carolina, M and José, N and Vanessa, B and Rubén, L}, title = {Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study.}, journal = {Journal of periodontal research}, volume = {60}, number = {9}, pages = {910-922}, doi = {10.1111/jre.13406}, pmid = {40202358}, issn = {1600-0765}, mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota/genetics ; *Metagenomics ; Female ; Male ; *Gingiva/microbiology ; Peru ; Chile ; Adult ; Spain ; Middle Aged ; Belgium ; Porphyromonas gingivalis/isolation & purification/genetics ; Tannerella forsythia/isolation & purification/genetics ; }, abstract = {AIMS: To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.

METHODS: In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.

RESULTS: The results indicated significant variation in α-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, β-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.

CONCLUSION: These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.}, } @article {pmid40987427, year = {2025}, author = {Hsu, BM and Chen, JS and Wang, WY and Chen, CJ and Fan, CW and Wu, CC and Hussain, B and Tsai, HC}, title = {An integral view of gut microbiome diversity and functional metabolic changes of a gut-brain axis associated with dementia based on metagenomic analysis.}, journal = {Physiology & behavior}, volume = {302}, number = {}, pages = {115112}, doi = {10.1016/j.physbeh.2025.115112}, pmid = {40987427}, issn = {1873-507X}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; *Dementia/microbiology/metabolism ; Middle Aged ; Female ; Aged ; Aged, 80 and over ; Metagenomics ; *Brain/metabolism ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Brain-Gut Axis/physiology ; }, abstract = {BACKGROUND: Growing evidence highlights the vital role by gut microbiota in brain health through the gut-brain axis, which involves neural, immune, endocrine, and metabolic signaling pathways. Disruption of this axis through microbial dysbiosis is increasingly linked to cognitive disorders, including dementia. However, the specific taxa and pathways involved remain poorly characterized. This study investigates taxonomic and functional shifts in the gut microbiome across healthy individuals, mild dementia, and dementia patients, aiming to identify microbial signatures and metabolic alterations associated with cognitive decline.

METHODS: A total of 184 participants (aged 60-98) were recruited and grouped into healthy, mild dementia, and dementia categories based on Clinical Dementia Rating scores. Demographic and clinical data were collected through structured interviews. Fecal samples were collected from participants and DNA was extracted and subjected to 16S rRNA gene sequencing. Sequencing data were processed using QIIME2 and classified using the SILVA database. Alpha (Shannon, Inverse Simpson) and beta diversity (Bray-Curtis PCoA) were analyzed between participant groups. Functional prediction was performed with PICRUSt2 to estimate KEGG orthologs from normalized ASVs. Statistical analyses were conducted in R using Kruskal-Wallis and PERMANOVA tests to assess group-level differences.

RESULTS: Dementia patients exhibited the highest proportion of unique ASVs (32.1 %) but showed reduced alpha diversity compared to mild dementia and healthy controls. PCoA revealed distinct microbial clustering across groups, explaining 19.3 % of total variance, with dementia samples forming a unique cluster. Taxonomically, dementia samples were enriched in Firmicutes and pro-inflammatory genera such as Peptoclostridium and Scardovia, while healthy controls harbored more SCFA-producing taxa like Lachnospiraceae_UCG-001. Co-occurrence networks in dementia were more complex, with increased inter-species connectivity and key drivers including Dorea and Clostridium innocuum. Functionally, dementia samples showed enrichment of vanillate degradation pathways and depletion of neuroprotective pathways like ergothioneine and vitamin E biosynthesis, correlating with specific microbial signatures.

CONCLUSIONS: Cognitive decline was associated with reduced microbial diversity and selective enrichment of pro-inflammatory taxa, reflecting gut ecological instability due to dementia. Microbial composition shifted progressively with dementia severity, indicating disease-specific gut microbial restructuring. Moreover, the loss of key functional microbial metabolites such as neuroprotective and anti-inflammatory metabolites supports targeting such metabolites and their producing gut microbiota as a therapeutic strategy for dementia. Future studies should ensure generalization by recruiting multi-center participants with strict guidelines for monitoring confounders.}, } @article {pmid40939728, year = {2025}, author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB}, title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.}, journal = {Physiology & behavior}, volume = {302}, number = {}, pages = {115102}, doi = {10.1016/j.physbeh.2025.115102}, pmid = {40939728}, issn = {1873-507X}, mesh = {Animals ; Male ; *Gastrointestinal Microbiome/drug effects/physiology ; *Physical Conditioning, Animal/physiology ; *Cardiovascular Diseases/prevention & control ; Rats ; *Arecaceae ; Liver/metabolism/drug effects ; Oxidative Stress/drug effects ; Rats, Wistar ; Fruit ; Blood Glucose ; Cholesterol/blood ; Heart Disease Risk Factors ; }, abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.

METHODOLOGY: Forty-four male rats were divided into four groups (n= 11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 min and progressing to 60 min. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.

RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.

CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.}, } @article {pmid41074769, year = {2025}, author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS}, title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf216}, pmid = {41074769}, issn = {1751-7370}, abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.}, } @article {pmid41074341, year = {2025}, author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z}, title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {220}, number = {}, pages = {117155}, doi = {10.1016/j.foodres.2025.117155}, pmid = {41074341}, issn = {1873-7145}, mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; }, abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.}, } @article {pmid41073886, year = {2025}, author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y}, title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {658}, pmid = {41073886}, issn = {1471-2180}, support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; }, mesh = {Animals ; Cattle/growth & development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration & dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; }, abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.}, } @article {pmid41072198, year = {2025}, author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E}, title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.}, journal = {The Science of the total environment}, volume = {1003}, number = {}, pages = {180681}, doi = {10.1016/j.scitotenv.2025.180681}, pmid = {41072198}, issn = {1879-1026}, abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.}, } @article {pmid40712732, year = {2025}, author = {Pérez-Molina, JA and Moreno, E and Crespillo-Andújar, C and Chamorro-Tojeiro, S and Arsuaga, M and Olavarrieta, L and Martín, O and Monge-Maillo, B and Norman, F and Lanza, VF and Serrano-Villar, S}, title = {Chagas disease induces gut microbial metabolic stress: Disruption of energy and nucleotide pathways and partial reversal by antiparasitic therapy (TRIPOBIOME-2 study).}, journal = {Travel medicine and infectious disease}, volume = {67}, number = {}, pages = {102881}, doi = {10.1016/j.tmaid.2025.102881}, pmid = {40712732}, issn = {1873-0442}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Chagas Disease/drug therapy/microbiology/metabolism ; Adult ; Male ; Female ; Middle Aged ; *Nitroimidazoles/therapeutic use ; Feces/microbiology ; Energy Metabolism ; *Nucleotides/metabolism ; Aged ; Trypanosoma cruzi ; Stress, Physiological ; }, abstract = {Chagas disease (CD) can alter gut microbiota composition, although its functional impact is poorly defined. We conducted whole-genome metagenomic sequencing of stool samples from 55 adults with chronic CD (23 treated with benznidazole) and 17 non-infected controls. Functional pathways were annotated with HUMAnN 3, and their differential abundance was assessed using ANCOM-BC2. Diversity metrics (Chao1/ACE indices and multidimensional scaling) and sPLS-DA modelling were used to explore community structure. No significant group differences were observed for alpha- and beta-diversity of bacterial functions; only 6-7 % of variance was attributable to infection status or prior benznidazole therapy. Nevertheless, chronic CD produced a distinctive functional signature marked by depletion of energy-yielding pathways (reductive and canonical tricarboxylic-acid cycles, fatty-acid β-oxidation, haem and 2-methylcitrate metabolism) and modest enrichment of purine and pyrimidine biosynthetic routes. These shifts may imply a microbiome adapting to hypoxia, nutrient scarcity, and metabolic competition with Trypanosoma cruzi. Compared with untreated patients and controls, benznidazole-treated individuals exhibited partial metabolic restoration, namely, up-regulated nucleotide and carbohydrate-degradation pathways, enhanced (5Z)-dodecenoate synthesis, and reduced reliance on the reductive tricarboxylic acid cycle, suggesting renewed microbial growth and improved short-chain-fatty-acid potential. Collectively, our results seem to portray a resource-limited, metabolically stressed gut ecosystem in chronic CD whose functional imbalance is partially reversible with antiparasitic therapy. The affected pathways, particularly those governing energy and nucleotide metabolism, could be used as candidate surrogate markers for disease monitoring and therapeutic response and as targets for microbiota-directed adjuvant strategies.}, } @article {pmid40662533, year = {2025}, author = {Jiang, J and Hu, D and Hu, S and Huang, K and Zheng, J and Pei, E}, title = {Age-Related Differences in Gut Microbiome and Fecal Metabolome of Captive African Penguins (Spheniscus demersus).}, journal = {Zoo biology}, volume = {44}, number = {5}, pages = {504-515}, doi = {10.1002/zoo.70014}, pmid = {40662533}, issn = {1098-2361}, support = {//This study was supported by a Project of Shanghai Zoo (SZ220302) and Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau (G250407)./ ; }, mesh = {Animals ; *Spheniscidae/microbiology/physiology ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolome/physiology ; Animals, Zoo/microbiology ; *Aging/physiology ; Age Factors ; Male ; }, abstract = {The purpose of the present study was to characterize the profiles of gut microbiota and fecal metabolites in African penguins (Spheniscus demersus) of different ages. The combination of metagenome and metabolome was performed on the feces of captive African penguins of varying age groups, including juvenile (1-3 years old), adult (4-15 years old) and senior (16-20 years old) individuals. The results of the metagenome showed that microbial abundance was significantly different between groups. Adult penguins had higher abundances of Gallilactobacillus and Ligilactobacillus compared to juvenile penguins. Senior penguins exhibited higher abundances of Gammaproteobacteria and Escherichia coli than adult penguins. We further identified differentially expressed metabolites across the groups using liquid chromatography-mass spectrometry analysis. Correlation analysis showed that age was correlated significantly with certain differential microbial species and fecal metabolites. The results revealed that age is a key factor influencing gut microbiota and metabolism in African penguins. Our results provide baseline information on gut microbial structure and fecal metabolite characteristics in African penguins of different ages, which is vital for the management and ex situ conservation of this endangered species.}, } @article {pmid41069707, year = {2025}, author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A}, title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf157}, pmid = {41069707}, issn = {2730-6151}, abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.}, } @article {pmid41068938, year = {2025}, author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S}, title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {345}, pmid = {41068938}, issn = {1474-760X}, support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; }, mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; }, abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.

RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.

CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.}, } @article {pmid41068590, year = {2025}, author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B}, title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {653}, pmid = {41068590}, issn = {1471-2180}, support = {2023ZSLC24//Zhongshan Hospital/ ; }, mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; }, abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.

METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.

RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio = 0.29; 95% confidence interval = 0.12-0.73; P = 0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score = 1.0; log2FoldChange = 3.6) and Dolosigranulum (NetMoss score = 0.6; log2FoldChange = 1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.

CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.}, } @article {pmid41068306, year = {2025}, author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X}, title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35375}, pmid = {41068306}, issn = {2045-2322}, support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; }, abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.}, } @article {pmid41031025, year = {2024}, author = {Waterworth, SC and Solomons, GM and Kalinski, JJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA}, title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41031025}, issn = {2692-8205}, abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.}, } @article {pmid40882788, year = {2026}, author = {Wu, J and Li, X and Huang, X and Zhu, Y and Yu, H and Xia, Y and Guo, S and Wang, X and Dong, T and Keung Tsim, KW and Zhu, Y}, title = {Kai-Xin-San, an ancient herbal mixture for anti-depression, mitigates the fluoxetine-induced gut dysbiosis and intestinal damage in chronic unpredictable mild stressed mice.}, journal = {Journal of ethnopharmacology}, volume = {354}, number = {}, pages = {120484}, doi = {10.1016/j.jep.2025.120484}, pmid = {40882788}, issn = {1872-7573}, mesh = {Animals ; *Fluoxetine/adverse effects/toxicity ; *Dysbiosis/chemically induced/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Depression/drug therapy/microbiology ; *Antidepressive Agents/pharmacology ; Intestines/drug effects/pathology ; Behavior, Animal/drug effects ; Disease Models, Animal ; }, abstract = {The gut microbiome plays a crucial role in the pathology of depression. The intestinal dysbiosis associated with prolonged use of antidepressants, such as fluoxetine, can adversely affect the efficacy of these medications. Kai-Xin-San (KXS), a traditional Chinese herbal decoction, has been utilized to treat mental disorders with a long history in China. The modulation of the gut microbiome by KXS could underlie its antidepressant effect. In the context of combining with fluoxetine, KXS could potentially mitigate fluoxetine-associated intestinal side effects during depression treatment.

AIM OF THE STUDY: This study investigates the impact of KXS on the gut of depressive mice, with a particular emphasis on its potential to mitigate fluoxetine-induced intestinal side effects.

MATERIALS AND METHODS: A high dose of fluoxetine was applied to the chronic unpredictable mild stress (CUMS)-induced mice, alone or in combination with KXS. Behavior tests were conducted to confirm the anti-depressant efficiencies. The feces of mice were collected and subjected to 16S rDNA and metagenomic sequencing. The gastrointestinal morphology and functions were assessed. The potential mechanistic action of KXS on alleviating the intestinal dysbiosis was probed.

RESULTS: Notable imbalance of microbiome and disruption of intestinal barrier were observed in CUMS mice. The intake of fluoxetine exacerbated the dysbiosis, as evidenced by the increased ratio of Firmicutes/Bacteroidetes and the elevated abundance of antibiotic-resistant genes in the gut microbiome. In addition, fluoxetine treatment further compromised the intestinal integrity and functions. Significantly, KXS treatment effectively mitigated the impairment of intestinal barrier induced by fluoxetine. These protective effects appeared to be mediated through multiple mechanisms, including the restoration of microbial homeostasis and the direct cytoprotective action on intestinal epithelial cells.

CONCLUSIONS: These findings particularly provide support for the combined usage of KXS and fluoxetine in depression treatment.}, } @article {pmid40883605, year = {2025}, author = {Yi, H and Lu, X and Chang, Q}, title = {MetaKSSD: boosting the scalability of the reference taxonomic marker database and the performance of metagenomic profiling using sketch operations.}, journal = {Nature computational science}, volume = {5}, number = {10}, pages = {884-897}, pmid = {40883605}, issn = {2662-8457}, mesh = {*Metagenomics/methods ; *Databases, Genetic ; Humans ; Microbiota/genetics ; Metagenome ; Software ; Computational Biology/methods ; Cluster Analysis ; }, abstract = {The performance of metagenomic profiling is constrained by the diversity of taxa present in the reference taxonomic marker database (MarkerDB) used. However, continually updating MarkerDB to include newly determined taxa using existing approaches faces increasing difficulties and will soon become impractical. Here we introduce MetaKSSD, which redefines MarkerDB construction and metagenomic profiling using sketch operations, enhancing MarkerDB scalability and profiling performance. MetaKSSD encompasses 85,202 species in its MarkerDB using just 0.17 GB of storage and profiles 10 GB of data within seconds. Leveraging its comprehensive MarkerDB, MetaKSSD substantially improves profiling results. In a microbiome-phenotype association study, MetaKSSD identified more effective associations than MetaPhlAn4. We profiled 382,016 metagenomic runs using MetaKSSD, conducted extensive sample clustering analyses and suggested potential yet-to-be-discovered niches. MetaKSSD offers functionality for instantaneous searching of similar profiles. It enables the swift transmission of metagenome sketches over the network and real-time online metagenomic analysis, facilitating use by non-expert users.}, } @article {pmid40695364, year = {2025}, author = {Kabil, AK and Liu, LT and Xu, C and Nayyar, N and González, L and Chopra, S and Brassard, J and Beaulieu, MJ and Li, Y and Damji, A and Zandstra, PW and Blanchet, MR and Hughes, MR and McNagny, KM}, title = {Microbial dysbiosis sculpts a systemic ILC3/IL-17 axis governing lung inflammatory responses and central hematopoiesis.}, journal = {Mucosal immunology}, volume = {18}, number = {5}, pages = {1139-1158}, doi = {10.1016/j.mucimm.2025.07.002}, pmid = {40695364}, issn = {1935-3456}, mesh = {Animals ; *Dysbiosis/immunology ; Mice ; *Interleukin-17/metabolism ; *Th17 Cells/immunology ; *Hematopoiesis ; *Lung/immunology ; Mice, Inbred C57BL ; Streptomycin ; Disease Models, Animal ; Microbiota ; Immunity, Innate ; }, abstract = {Advancements in vaccination and sanitation have significantly reduced the prevalence and burden of infectious diseases; however, these benefits have coincided with a marked rise in autoimmune and allergic disorders. Recent studies have investigated these linked trends through the lens of host-microbiome alterations, proposing these shifts as a potential explanatory mechanism. Previously, we demonstrated that vancomycin-induced depletion of short-chain fatty acid (SCFA) producing bacteria results in hyperactivation of ILC2s and exacerbated allergic responses. Here we investigate the effects of low-dose streptomycin on innate and adaptive immune cell populations and their activation states. Although streptomycin-treated mice exhibit normal allergic responses, they display heightened susceptibility to Th1/Th17-mediated disease, specifically hypersensitivity pneumonitis (HP). This is characterized by a two-fold increase in ILC3s and Th17 cells in the lungs, alongside activation of antigen-presenting cells (APCs) at steady state, an effect that is further amplified upon exposure to HP-inducing agents. Shotgun metagenomic analysis revealed that streptomycin-induced dysbiosis reduces microbial diversity, depletes bile acid-metabolizing bacteria, and enriches for metabolic pathways involved in branched-chain amino acid biosynthesis, including leucine, a known activator of mTORC1. Strikingly, administration of the secondary bile acid metabolite isolithocholic acid (an inverse agonist of RORγt), or an IL-23 neutralizing antibody, reverses the enhanced susceptibility to HP. Inhibition of mTORC1 also significantly reduced Th17/ILC3 responses and histopathology. Our findings underscore microbial equilibrium as a key determinant of susceptibility to HP and uncover a positive feedback loop between IL-23-producing APCs and ILC3/Th17 cells that mechanistically links dysbiosis to sustained type 3 inflammation; and we identify a simple, actionable means of intervention.}, } @article {pmid41068233, year = {2025}, author = {Giovannini, N and Limena, A and Ercolino, C and Renteria, SCU and Strati, F and Giuffrè, MR and Maragno, P and Carbone, IF and Facciotti, F and Ceriotti, F and Ferrazzi, E and Lattuada, D}, title = {Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35306}, pmid = {41068233}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *COVID-19/microbiology/virology ; *Nasopharynx/microbiology ; Adult ; *Microbiota ; *Mouth/microbiology ; SARS-CoV-2/isolation & purification ; *Pregnancy Complications, Infectious/microbiology/virology ; }, abstract = {Variations have been found in the upper respiratory tract microbiota in SARS-CoV-2 positive patients compared to healthy subjects, with different dominant species and diversity indexes detected, including a decrease in biodiversity and an increased abundance of bacterial pathogens. Moreover, these discrepancies were observed in patients with both mild and severe symptoms. Notably, the inflammatory state appears to be significantly influenced by the characteristics of the indigenous microbiota. This is particularly interesting in pregnant patients, as pregnancy involves an adaptive adjustment of the microbiota due to hormonal changes aimed at providing immune protection. The relationship between the microbiota of pregnant women and SARS-CoV-2 has not been deeply explored so far. The purpose of the present study is to investigate the relationship between SARS-CoV-2, nasopharyngeal and oral microbiota, and pregnancy. To our knowledge this is the first simultaneous investigation on both nasopharyngeal and oral microbiota in SARS-Cov-2 infected pregnant women. In this study, the nasopharyngeal and oral microbiota were analysed in 43 women in their third trimester of pregnancy enrolled from April 2020 to February 2021. The differential abundance of taxa was tested and alpha and beta diversity were evaluated. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. In both the nasopharyngeal and oral microbiota of the SARS-CoV-2 infected pregnant women, we found a variation in taxa, represented by an enrichment of pathobionts, which increased particularly with the severity of symptoms. Specifically, a significant reduction in microbial biodiversity has been identified within the nasopharyngeal microbiota of SARS-CoV-2 positive women. Furthermore, enrichment in pathobionts was noted in both asymptomatic and symptomatic women, with these changes being more pronounced in the nasopharyngeal microbiota compared to the oral one. The nasopharyngeal microbiota of asymptomatic and symptomatic SARS-CoV-2 infected women showed an enrichment of pathogens and pathobionts such as Corynebacterium, Fusobacterium, Neisseria, Streptococcus, Haemophilus, Mycobacterium and Porphyromonas compared with the control group. The oral microbiota showed an enrichment of pathobionts such as Neisseria, Fusobacterium and Streptococcus. A random forest classifier applied to metagenomic data from nasopharyngeal and oral swabs showed that the nasopharyngeal microbiota is the best sampling site to predict the patients' SARS-CoV-2 infection status. Gulbenkiania, Burkholderia and Actinomyces, all taxa significantly enriched in the control group compared to SARS-CoV-2 infected women, were the most important features selected by the classifier. Finally, correlations between the nasopharyngeal and oral microbiota and clinical parameters of pregnant women, particularly BMI and procalcitonin, were observed. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. We found a variation in taxa, represented by the enrichment of pathobionts in both the nasopharyngeal and oral microbiota of SARS-CoV-2 infected pregnant women, particularly increased in symptomatic individuals. The nasopharyngeal microbiota appears to be a better predictor of SARS-CoV-2 infection and its severity than the oral microbiota.}, } @article {pmid41068119, year = {2025}, author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y}, title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {196}, pmid = {41068119}, issn = {2055-5008}, support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; }, abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.}, } @article {pmid41066275, year = {2025}, author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, S}, title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.}, journal = {Journal of medical microbiology}, volume = {74}, number = {10}, pages = {}, doi = {10.1099/jmm.0.002065}, pmid = {41066275}, issn = {1473-5644}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Periodontitis/therapy/microbiology ; Middle Aged ; Adult ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; }, abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.}, } @article {pmid41066109, year = {2025}, author = {Zhou, T and Delgado-Baquerizo, M and Ren, C and He, N and Zhou, Z and He, Y}, title = {Soil microbial life history strategies covary with ecosystem multifunctionality across aridity gradients.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {41}, pages = {e2511071122}, doi = {10.1073/pnas.2511071122}, pmid = {41066109}, issn = {1091-6490}, support = {202206600027//China Scholarship Council (CSC)/ ; 32522067//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Ecosystem ; *Desert Climate ; Soil/chemistry ; }, abstract = {Aridity thresholds shape ecosystem functions worldwide. Despite the importance of soil microbiomes in engineering ecosystem processes, the specific strategies employed by soil microbiomes to support ecosystem multifunctionality (EMF) across aridity gradients remain virtually unknown. Here, we investigated 474 soil samples across a continental-scale aridity gradient and identified an aridity threshold beyond which plot-level EMF declines sharply. Microbial habitat and decomposition functions were among the last to respond to aridity, with thresholds occurring under more arid conditions compared to plant productivity and soil fertility. Combining metagenomic sequencing with physiological assays to characterize microbial life history strategies of high yield (Y), resource acquisition (A), and stress tolerance (S), we introduce a microbial trait-based framework to mechanistically link community-level microbial life history strategies to EMF. Our results reveal that microbial Y-strategy is positively correlated with EMF across aridity gradients, A-strategy exhibits a negative association with EMF across aridity gradients, and S-strategy is negatively correlated with EMF in arid ecosystems. Collectively, this study offers empirical evidence and insights into how aridification interacts with soil microbiomes in shaping EMF, highlighting the pivotal role of microbial life history strategies in understanding the mechanisms behind EMF variation in an increasingly arid world.}, } @article {pmid41062579, year = {2025}, author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J}, title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35107}, pmid = {41062579}, issn = {2045-2322}, support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; }, mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Microbiota ; }, abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.}, } @article {pmid41062543, year = {2025}, author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L}, title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35039}, pmid = {41062543}, issn = {2045-2322}, mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; }, abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.}, } @article {pmid41062510, year = {2025}, author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X}, title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8934}, pmid = {41062510}, issn = {2041-1723}, support = {R15LM013460//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; }, mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; }, abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.}, } @article {pmid41062486, year = {2025}, author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B}, title = {Node role of wild boars in virus circulation among wildlife and domestic animals.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8938}, pmid = {41062486}, issn = {2041-1723}, mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; }, abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.}, } @article {pmid41059690, year = {2025}, author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A}, title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0129125}, doi = {10.1128/spectrum.01291-25}, pmid = {41059690}, issn = {2165-0497}, abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.}, } @article {pmid41059040, year = {2025}, author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q}, title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1637352}, pmid = {41059040}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; }, abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.

METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by α-diversity, β-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.

RESULTS: Overall, no significant differences in viral and bacterial α- or β-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.

CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.}, } @article {pmid41058503, year = {2025}, author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA}, title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.}, journal = {Journal of the Royal Society, Interface}, volume = {22}, number = {231}, pages = {20250183}, doi = {10.1098/rsif.2025.0183}, pmid = {41058503}, issn = {1742-5662}, support = {//Agencia Estatal de Investigación/ ; }, mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; }, abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.}, } @article {pmid41056245, year = {2025}, author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N}, title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0333676}, pmid = {41056245}, issn = {1932-6203}, mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; }, abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.}, } @article {pmid40985550, year = {2025}, author = {He, Y and Baltar, F and Wang, Y}, title = {Seasonal variability in community structure and metabolism of active deep-sea microorganisms.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf214}, pmid = {40985550}, issn = {1751-7370}, support = {ZDSYS20230626091459009//Shenzhen Key Laboratory of Advanced Technology for Marine Ecology/ ; //National Natural Science Foundation of China/ ; }, mesh = {*Seasons ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; China ; *Microbiota ; Archaea/classification/metabolism/genetics ; Metagenome ; }, abstract = {Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA degradation and microbial community shifts. Here, we employed an in situ DNA/RNA co-extraction device to collect 18 time-series nucleic acid samples during winter and summer in the South China Sea, minimizing sampling perturbation for metatranscriptome and metagenome analyses. Between the two seasons, the prokaryotic microbiota showed seasonal variations in species composition. Burkholderiales dominated in summer, whereas Pseudomonadales, Bacillales, and Rhodobacterales were enriched in winter. However, the dominant transcriptionally active taxa affiliated with Nitrososphaerales, MGIII, SAR324, UBA11654, Marinisomatales, and Poseidoniales remained largely stable across seasons. Among eukaryotes, Ciliophora were the most active, whereas Retaria were abundant but inactive. Despite the stable active prokaryotic community, metabolic profiles differed significantly between seasons. In the winter, autotrophic microorganisms, particularly Nitrososphaerales, exhibited higher CO2 fixation activity via the 3HP/4HB cycle, accompanied by enhanced ammonia oxidation for energy generation. In addition, CO oxidation activity was also elevated. In the summer, the primary source of energy originated from heterotrophic microorganisms capable of utilizing fatty acids, benzoate, and H2, likely relying on anaerobic respiration within organic particles. This may relate to nutrient source variations as reflected by the different levels of microbial network complexity between the two seasons. Altogether, our in situ metatranscriptomes revealed the metabolic activities and adaptations of active microbial groups across seasons, providing a basis for identifying the microbial contributors to elemental cycles in the deep ocean.}, } @article {pmid40972887, year = {2025}, author = {Hitch, TCA and Bosch, J and Bolsega, S and Deschamps, C and Etienne-Mesmin, L and Treichel, N and Blanquet-Diot, S and Ocvirk, S and Basic, M and Clavel, T}, title = {Function-based selection of synthetic communities enables mechanistic microbiome studies.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf209}, pmid = {40972887}, issn = {1751-7370}, support = {CA23110//European Union, COST action INFOGUT/ ; 513892404//German Research Foundation/ ; 460129525//German Research Foundation/ ; NFDI4Microbiota//German Research Foundation/ ; 403224013//German Research Foundation/ ; SFB1382//German Research Foundation/ ; 395357507//German Research Foundation/ ; SFB1371//German Research Foundation/ ; 01KA2103//German Federal Ministry of Education and Research/ ; }, mesh = {Animals ; Mice ; Humans ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; *Host Microbial Interactions ; Metagenome ; Germ-Free Life ; *Gastrointestinal Microbiome ; Colitis/microbiology ; }, abstract = {Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.}, } @article {pmid40956094, year = {2025}, author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA}, title = {Profiling bile acids in the stools of humans and animal models of cystic fibrosis.}, journal = {Microbiology spectrum}, volume = {13}, number = {10}, pages = {e0145125}, pmid = {40956094}, issn = {2165-0497}, support = {ES 033988-01A1/NH/NIH HHS/United States ; 05912G223//Cystic Fibrosis Foundation/ ; T32HL134598/NH/NIH HHS/United States ; R01AI164772, U01AI163063, P30DK117469/NH/NIH HHS/United States ; P20-GM130454/NH/NIH HHS/United States ; }, mesh = {*Cystic Fibrosis/microbiology/metabolism ; Animals ; *Bile Acids and Salts/metabolism/analysis ; *Feces/chemistry/microbiology ; Humans ; Mice ; Disease Models, Animal ; Ferrets ; Male ; Gastrointestinal Microbiome ; Female ; Child ; Bacteria/classification/genetics/metabolism/isolation & purification ; Child, Preschool ; Adolescent ; }, abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with aberrant bile acid (BA) metabolism. As little is known about BA in children with CF (cwCF), we performed both comprehensive (n = 89) and focused (n = 21) BA profiling in stool of children with or without CF. Our results reveal select BA species and metabolites are significantly different between cwCF and nonCF controls. Focused BA profiling revealed a significant increase in total BA levels and selected changes in a subset of BA classes for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in this small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroidetes (lower in cwCF) phylum are consistent with prior reports. A trend was noted toward reduced abundance of bsh gene families, a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Observed modest changes in both BAs and microbial BA metabolism-related gene abundances may suggest a possible combination of defects in host and microbial BA metabolic pathways in cwCF. Fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, and while the ferret model reproduced significant differences between CF and nonCF animals, the nonCF animals showed higher levels of BA (opposite of what is observed in humans), indicating that neither model recapitulated BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF and highlight limitations of CF animal models for BA functional studies.

IMPORTANCE: Changes in the abundance and/or composition of intestinal BAs may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for cwCF. Matched metagenomic analysis suggests possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.}, } @article {pmid40914155, year = {2025}, author = {Muñoz, VR and Moreau, F and Soto, M and Watanabe, Y and Pham, LD and Zhong, J and Zimmerman, S and Brandao, BB and Girdhar, K and Avila, J and Pan, H and Dreyfuss, JM and Mi, MY and Gerszten, RE and Altindis, E and Kostic, A and Clish, CB and Kahn, CR}, title = {Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.}, journal = {Cell metabolism}, volume = {37}, number = {10}, pages = {2048-2065.e6}, doi = {10.1016/j.cmet.2025.08.005}, pmid = {40914155}, issn = {1932-7420}, mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; Diet, High-Fat/adverse effects ; Male ; Humans ; *Portal Vein/metabolism ; Gluconeogenesis ; Hepatocytes/metabolism/drug effects ; Vancomycin/pharmacology ; Liver/metabolism ; Obesity/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Diet and obesity contribute to insulin resistance and type 2 diabetes, in part via the gut microbiome. To explore the role of gut-derived metabolites in this process, we assessed portal/peripheral blood metabolites in mice with different risks of obesity/diabetes, challenged with a high-fat diet (HFD) + antibiotics. In diabetes/obesity-prone C57BL/6J mice, 111 metabolites were portally enriched and 74 were peripherally enriched, many of which differed in metabolic-syndrome-resistant 129S1/129S6 mice. Vancomycin treatment of HFD-fed C57BL/6J mice modified the microbiome and the portal/peripheral ratio of many metabolites, including upregulating tricarboxylic acid (TCA) cycle-related metabolites, like mesaconate, in portal blood. Treatment of isolated hepatocytes with mesaconate, itaconate, or citraconate improved insulin signaling and transcriptionally regulated genes involved in gluconeogenesis, fatty acid oxidation, and lipogenesis in vitro and in vivo. In humans, citraconate levels are inversely correlated with plasma glucose. Thus, portal versus peripheral metabolites play important roles in mediating effects of the microbiome on hepatic metabolism and the pathogenesis of HFD-related insulin resistance.}, } @article {pmid40862625, year = {2025}, author = {Ao, J and Tang, X and Li, Z and Tang, Z}, title = {Shrub encroachment alters microbial community composition and soil carbon and nitrogen cycling functional genes in northern peatlands.}, journal = {Microbiology spectrum}, volume = {13}, number = {10}, pages = {e0054225}, pmid = {40862625}, issn = {2165-0497}, support = {2023YFF1304604-3//National Key Research and Development Program of China/ ; XZ202401ZY0110//Key R&D Program of Tibet Autonomous Region, China/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; Wetlands ; *Microbiota/genetics ; Fungi/genetics/classification/metabolism/isolation & purification ; Carbon Cycle/genetics ; Nitrogen Fixation/genetics ; Ecosystem ; }, abstract = {Changes in vegetation, such as shrub encroachment in grassland and wetland ecosystems, significantly influence soil microbial communities and biogeochemical processes. However, the specific impact of shrub encroachment on peatland ecosystems remains poorly understood. This study used a "space-for-time" approach, collecting soil samples from three encroachment stages-uninvaded, shrub invasion, and shrub invasion expansion-at two depths (0-30 cm and 30-60 cm). Metagenomic sequencing was used to assess the microbial community composition and functional gene dynamics. Shrub encroachment significantly alters soil physicochemical properties, nutrient availability, and microbial communities. Alpha diversity of bacteria and fungi was influenced by shrub encroachment and depth, whereas beta diversity varied mainly with depth. Functional carbon fixation genes (korA and pps) increased during shrub encroachment, while methane oxidation (hdrA2) and carbon degradation genes (GH31 and GH51) decreased before increasing. In addition, functional genes linked to nitrogen cycling (nifD, nifH, amoA, and amoC) declined, indicating a reduction in nitrogen fixation and nitrification pathways. Correlation and Mantel tests revealed that the total soil carbon content was the primary driver of these functional changes. These findings highlight the dynamic microbial responses to shrub encroachment and offer insights into the soil carbon and nitrogen-cycling mechanisms in peatlands.IMPORTANCEShrub encroachment is transforming peatlands and altering their ecological and biogeochemical functions. This study provides critical insights into how shrub invasion affects microbial communities and functional genes responsible for carbon and nitrogen cycling in peatland soils. By revealing the underlying genetic mechanisms, this study enhances our understanding of the consequences of vegetation shifts on ecosystem processes. These findings are essential for predicting and managing peatland responses to environmental changes, helping to preserve their role as vital carbon and nutrient reservoirs.}, } @article {pmid40833093, year = {2025}, author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R}, title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.}, journal = {Microbiology spectrum}, volume = {13}, number = {10}, pages = {e0311924}, pmid = {40833093}, issn = {2165-0497}, mesh = {*Metagenomics/methods/standards ; Humans ; *High-Throughput Nucleotide Sequencing/methods/standards ; *DNA Contamination ; *Microbiota/genetics ; Workflow ; *DNA, Bacterial/genetics/isolation & purification ; Indicators and Reagents ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.}, } @article {pmid41056240, year = {2025}, author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS}, title = {Dysglycemia and the airway microbiome in cystic fibrosis.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0331847}, doi = {10.1371/journal.pone.0331847}, pmid = {41056240}, issn = {1932-6203}, mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; }, abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).

METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.

RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p = 0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p = 0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p = 0.056 and 1.11 [0.58, 1.64] unadjusted p= < .001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p = 0.001 for each 10% increase in virome score).

CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.}, } @article {pmid41053318, year = {2025}, author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC}, title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {34702}, pmid = {41053318}, issn = {2045-2322}, support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; }, mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; }, abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.}, } @article {pmid40919785, year = {2025}, author = {Zou, Y-y and Yu, B-j and He, C and Ding, L and Xu, X and Wan, J-h and Lei, Y-p and Huang, X and Xiong, H-f and He, W-h and Luo, L-y and Xia, L and Lv, N-h and Zhu, Y}, title = {Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.}, journal = {Microbiology spectrum}, volume = {13}, number = {10}, pages = {e0129925}, doi = {10.1128/spectrum.01299-25}, pmid = {40919785}, issn = {2165-0497}, support = {No.82370661//National Natural Science Foundation of China/ ; YFYKCTDPY202202//Science and Technology Innovation Team Cultivation Project of the First Affiliated Hospital of Nanchang University/ ; }, mesh = {Animals ; *Rifaximin ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; Humans ; Disease Models, Animal ; Female ; *Pancreatitis/drug therapy/microbiology/pathology ; Middle Aged ; *Inflammation/drug therapy ; Adult ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; }, abstract = {UNLABELLED: Severe acute pancreatitis (SAP) is characterized by systemic inflammation and intestinal barrier dysfunction and is often associated with gut microbiota dysbiosis. Rifaximin, a gut-specific non-absorbable antibiotic, is known to modulate the gut microbiota. Here, we investigated rifaximin's effects and mechanisms in SAP using murine models and a single-center, open-label, randomized controlled trial (Chinese Clinical Trial Registry: ChiCTR2100049794). In mice, rifaximin attenuated pancreatic injury and systemic inflammation and altered gut microbiota composition by decreasing mucin-degrading genera such as Akkermansia (P < 0.05). These protective effects persisted in antibiotic-treated and germ-free mice, suggesting mechanisms not solely dependent on gut microbiota modulation. In patients with predicted SAP (n = 60), rifaximin significantly reduced systemic inflammation compared with controls. WBC decreased from a median of 11.50 × 10[9]/L (IQR 8.76-15.68) to 8.49 × 10[9]/L (6.93-10.20; P = 0.04) and TNF-α from 15.05 pg/mL (12.73-19.75) to 11.00 pg/mL (8.74-15.40; P = 0.009). However, the incidence of culture-confirmed infection did not differ between the rifaximin and control groups (13.3% vs. 13.3%; RR, 1.00; 95% CI, 0.28-3.63). Adverse events were comparable between groups. Metagenomic analyses revealed suppression of mucin-degrading bacteria (e.g., Akkermansia, Bacteroides fragilis, and Hungatella hathewayi) (P < 0.05) and reductions in mucin-degrading carbohydrate-active enzymes, including sialidases and fucosidases. In conclusion, among patients with predicted SAP, rifaximin did not reduce culture-confirmed infectious complications within 90 days after randomization compared with standard care, despite significant improvements in systemic inflammatory markers and selected fecal microbiome features. Larger randomized controlled trials are warranted to validate these findings.

IMPORTANCE: Although rifaximin has been used to target gut-derived inflammation in other contexts, its role in SAP remains largely unexplored. In this study, rifaximin treatment was associated with reduced pancreatic injury and systemic inflammation in both murine models and patients with predicted SAP. Treatment also led to changes in gut microbial composition, notably a decrease in mucin-degrading taxa. Importantly, similar protective effects were also observed in antibiotic-treated and germ-free mice, indicating that rifaximin may act via microbiota-dependent and host-directed pathways. These findings offer novel insights into the gut-pancreas axis and suggest that rifaximin holds therapeutic potential by modulating gut microbial composition and host inflammatory responses in SAP.}, } @article {pmid40915262, year = {2025}, author = {Liu, S and Feng, K and Zhang, D and Liu, Y and Wang, J and Lu, B and Xing, D}, title = {Self-regulating adaptability of biofilm microbiomes enhances manganese and ammonia removal in microbial electrochemical filters under dioxane exposure.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139776}, doi = {10.1016/j.jhazmat.2025.139776}, pmid = {40915262}, issn = {1873-3336}, mesh = {*Biofilms ; *Ammonia/metabolism ; *Microbiota ; *Manganese/metabolism ; *Dioxanes ; *Water Pollutants, Chemical/metabolism ; Filtration ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Electrochemical Techniques ; Water Purification/methods ; }, abstract = {Understanding the stability and assemblage of biofilm microbiomes under oligotrophic conditions is critical for improving groundwater bioremediation. In this study, a novel microbial electrochemical filter (MEF) was developed to explore the impact of weak electrical stimulation on functional adaptability of biofilms under oligotrophic and 1,4-dioxane exposure conditions. Under 20 mg/L 1,4-dioxane stress, the MEF achieved 94.72 % manganese removal and 27.27 % ammonia nitrogen removal, while the conventional biofilter exhibited 88.76 % manganese removal with negligible ammonia nitrogen removal. Metagenomics analyses revealed that dominant populations in the MEF included Nitrospira, Bradyrhizobium, and Nitrosomonas, with relative abundance of 6.23 -10.78 %, 5.81 -6.15 %, and 1.62 -5.58 %, respectively. Weak electrical stimulation enriched the manganese oxidation-associated genes cotA, mnxG, and mcoA, whose total relative abundances being 6.3 times that of the conventional biofilter before dioxane exposure and 2.0 times after exposure. Genes encoding ammonia monooxygenase (amoABC), hydroxylamine dehydrogenase (hao) increased by 2.4- and 1.9-fold, respectively, compared to the conventional biofilter. Additionally, genes involved in the reductive tricarboxylic acid cycle and nitrogen fixation were twice as abundant in the MEF than in the conventional biofilter, suggesting enhanced nutrients availability for heterotrophic bacteria during start-up. These findings demonstrated that weak electrical stimulation effectively regulated biofilm microbiomes and enhance pollutant removal in MEF under oligotrophic conditions.}, } @article {pmid40910779, year = {2025}, author = {Hanawa, S and Son, A and Kato, T and Matsuo, Y and Omae, T and Omori, Y and Yoshikawa, K and Yamanegi, K and Hirota, K and Ohno, H and Ogura, H and Ishido, S and Noguchi, K and Kishimoto, H}, title = {Identification of beneficial symbiont candidates in commensalism as potential oral gatekeepers.}, journal = {Microbiology spectrum}, volume = {13}, number = {10}, pages = {e0158825}, doi = {10.1128/spectrum.01588-25}, pmid = {40910779}, issn = {2165-0497}, support = {JP23H05357//Japan Society for the Promotion of Science/ ; JP22K09106//Japan Society for the Promotion of Science/ ; //Hyogo College of Medicine/ ; }, mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; Microbiota ; Male ; Female ; *Mouth Neoplasms/microbiology ; Middle Aged ; Probiotics ; *Bacteria/classification/genetics/isolation & purification ; Adult ; RNA, Ribosomal, 16S/genetics ; Healthy Volunteers ; Aged ; Dysbiosis/microbiology ; }, abstract = {The basis of the development of oral cancer has been reported to be inflammation (e.g., periodontitis) caused by dysbiosis of the oral microbiota (i.e., a decrease in beneficial oral symbionts). Since a decrease in beneficial symbionts is connected to oral cancer, restoring these bacteria may help prevent it. Based on this, oral probiotics using beneficial oral symbionts are under development. Therefore, it is necessary to understand how beneficial oral symbionts are maintained in a healthy oral cavity. We evaluated a cohort consisting of 42 healthy volunteers and 39 oral cancer patients via 16S metagenomic analysis. Beneficial symbiont candidates were mined by comparing the oral microbiota of healthy volunteers with that of oral cancer patients, and the interaction mode among the beneficial symbiont candidates was further examined. Cancer patients exhibited decreased relative abundance of the genera Rothia and Streptococcus. In addition, both bacterial genera further decreased in advanced cancer, highlighting them as beneficial candidates. Furthermore, these two bacterial genera demonstrated a positive correlation in terms of relative abundance. Rothia dentocariosa isolated from a representative healthy volunteer was suggested to support the survival of Streptococcus salivarius through possible syntrophic interaction. Thus, we report a potential syntrophic interaction between Streptococcus spp. and Rothia spp. as a possible mechanism underlying oral health maintenance. Given that S. salivarius is currently employed as an oral probiotic, our findings provide insights into the development of probiotics for oral cancer.IMPORTANCEPathobiont candidates associated with oral cancer are currently being thoroughly investigated. However, it is not clear which bacteria and how their interactions contribute to preventing the development of oral cancer. In this report, we demonstrate for the first time the presence of a potential syntrophic interaction between Rothia spp. and Streptococcus spp., both of which were identified as beneficial symbiont candidates in the oral cavity.}, } @article {pmid40886530, year = {2025}, author = {Miao, L and Ma, T and Qi, J and Deng, Y and Hong, Y and Gong, X and Zang, H and Cheng, Y and Li, C}, title = {Deciphering intrakingdom synergism in 17β-estradiol degradation through DNA-SIP coupled metagenomics: Metabolic cooperation and niche partitioning in bioaugmented soil microbiomes.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139709}, doi = {10.1016/j.jhazmat.2025.139709}, pmid = {40886530}, issn = {1873-3336}, mesh = {Metagenomics ; *Soil Microbiology ; Biodegradation, Environmental ; *Estradiol/metabolism ; *Microbiota ; Rhodococcus/metabolism/genetics ; *Soil Pollutants/metabolism ; Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; }, abstract = {17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310-1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter, Mycobacterium, Rhodococcus, Sphingomonas, and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole timeflight mass spectrometry (HPLCQTOFMS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track [13]C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.}, } @article {pmid40882374, year = {2025}, author = {Chen, Y and Zhang, Y and Li, J and Li, Y and Chen, Z and Qin, J and Deng, Z and Wang, X}, title = {Fe(Ⅱ)-mediated detoxification mitigates low-dose rare earth elements-induced stress on anammox consortia for mining tailwater treatment.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139681}, doi = {10.1016/j.jhazmat.2025.139681}, pmid = {40882374}, issn = {1873-3336}, mesh = {Mining ; *Metals, Rare Earth/toxicity ; *Water Pollutants, Chemical/toxicity/metabolism ; Bioreactors ; *Microbial Consortia/drug effects ; Wastewater ; *Ferrous Compounds/chemistry ; Biodegradation, Environmental ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; Water Purification/methods ; *Iron ; }, abstract = {Rare earth mining activities cause severe nitrogen pollution in watersheds, yet the residual hazardous rare earth elements (REEs) toxicity in tailings wastewater challenges biological nitrogen removal technology. This work demonstrated that introducing low-dose Fe(II) into partial denitrification/anammox (PD/A) system significantly alleviated REEs-induced stress on anammox consortia via detoxification and physical barrier reinforcement. The PD/A bioreactor with 15 mg/L Fe(II) (R1) was compared against a control without Fe(II) for real rare earth tailings wastewater treatment. Metagenomic analysis identified 1.14-fold upregulation of hydrazine (N2H4) dehydrogenase alongside substantial 5.82-fold downregulation of N2H4 synthase in R1, indicating a critical metabolic reconfiguration that expedited the degradation of toxic intermediates and alleviated REEs-mediated cytotoxicity. Electrons with lower redox potential released from N2H4 oxidation were more effectively utilized for carbon fixation, as evidenced by the upregulated electron transport complexes and Wood-Ljungdahl pathway. Concurrent biosynthetic modulation stimulated lipopolysaccharide production (module M00063) and carbohydrate storage (module M00064), collectively reinforcing microbial stress resilience through both defensive metabolites (lipopolysaccharides and trehalose) and hydrophobicity-driven aggregation. Moreover, modified 2-P logistic modeling confirmed elevated REEs inhibition thresholds under Fe(II) mediation. This study reveals the defense mechanism of Fe(II)-enhanced anammox consortia against REEs stress, providing new insights for sustainable bioremediation in rare earth mining areas.}, } @article {pmid40865218, year = {2025}, author = {Yang, H and Fu, H and Zhao, Y and Li, R and Cao, M and Liu, Y and Ni, Y and Song, W and Liang, Y and Cai, P and Chang, W and Tao, F and Wang, H and Liu, K}, title = {Antibiotic resistance genes in multi-matrices of Chaohu Lake: Spatiotemporal variation and correlation with pesticides and PPCPs.}, journal = {Journal of hazardous materials}, volume = {497}, number = {}, pages = {139604}, doi = {10.1016/j.jhazmat.2025.139604}, pmid = {40865218}, issn = {1873-3336}, mesh = {*Lakes/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; *Pesticides/analysis ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; *Genes, Bacterial ; Geologic Sediments/microbiology ; Animals ; Pharmaceutical Preparations/analysis ; Microbiota ; Spatio-Temporal Analysis ; Fishes ; China ; }, abstract = {This study explored the spatiotemporal distributions of microorganisms and antibiotic resistance genes (ARGs) in the surface water, sediments, and fish intestinal contents (IC) of Chaohu Lake, and further revealed the pharmaceuticals and personal care products (PPCPs), pesticides in lake water and their relationships with ARGs. 53 types of pesticides and 25 types of PPCPs were identified in the river-lake system basin, with the highest concentrations observed for tebuconazole (1142.36 ng/L) and amantadine (851.41 ng/L). Higher concentrations of these target contaminants were detected in the western part of the lake and during the wet season. No significant east-west differences in ARGs and microbiota across the three environmental matrices were found, whereas seasonal variations impacted lake water and IC more profoundly than sediments. Significant correlations between microbiota and ARGs in the lake water and IC, while those in sediments showed weaker associations. Co-occurrence network analysis showed, among three environmental media, β-lactam and multidrug-resistant genes were widespread found, and Proteobacteria were identified as a stable host. Non-antibiotic pollutants, such as amantadine and terbuthylazine, displayed significant positive correlations with ARGs, similar to sulfamethoxazole and clindamycin. Our findings highlight the important roles of seasonal hydrological changes and non-antibiotic pollutants in the dissemination of ARGs.}, } @article {pmid40824084, year = {2025}, author = {Li, J and Liang, L and Ye, J and Miao, Y and Zhao, K and Tian, Y and Li, X and Li, X and Chen, X and Wen, B and He, Y and Chen, B and Qin, L and Wang, Y and Fu, X}, title = {Gastric microbiota transplantation enhanced the eradication of refractory Helicobacter pylori infection by modulating the gastric microbiota: a pilot study.}, journal = {Microbiology spectrum}, volume = {13}, number = {10}, pages = {e0326324}, doi = {10.1128/spectrum.03263-24}, pmid = {40824084}, issn = {2165-0497}, support = {2024ZYD0144 and 24ZYZYTS0389//Central Government-Directed Project for Local Science and Technology Development/ ; 24WXXT05//Health Commission of Sichuan Province/ ; }, mesh = {Humans ; *Helicobacter Infections/therapy/microbiology ; Pilot Projects ; *Helicobacter pylori ; Male ; Middle Aged ; Female ; Adult ; Gastric Mucosa/microbiology ; *Gastrointestinal Microbiome ; Gastritis, Atrophic/therapy/microbiology ; *Stomach/microbiology ; Aged ; Dysbiosis/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {UNLABELLED: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. In this study, we investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. We performed a metagenomic analysis of the microecological systems across different regions of the stomach, including the gastric fluid (GF), the gastric mucus layer (GML), and the gastric mucosa (GM). We initiated a clinical GMT intervention by transplanting microbial communities from healthy individuals' GML into patients exhibiting refractory H. pylori infection and chronic atrophic gastritis. Our findings demonstrated significant disparities in species richness among the GF, GML, and GM, with the GML exhibiting the highest diversity of unique microbial genera. H. pylori infection primarily influenced the relative species abundance within the GML community, without altering its fundamental composition. Clinically, GMT was well-tolerated by all recipients and showed substantial synergistic efficacy against refractory H. pylori infection, achieving a 100% eradication rate in all patients, and significantly alleviating symptoms in individuals with H. pylori-positive atrophic gastritis (P < 0.05). Compared with the gastric microbiota of H. pylori-negative patients, the gastric microbiota of H. pylori-positive patients treated with GMT exhibited closer alignment with those of healthy donors. In conclusion, GMT utilizing GML enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis through modulating the gastric microbiota.

IMPORTANCE: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. We investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. GMT significantly enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis. GMT demonstrated improvements in the cure rate of refractory H. pylori infection, potentially offering a new clinical treatment approach. This finding provides new insights and a potential therapeutic direction for treating dysbiosis related chronic gastric diseases.}, } @article {pmid41052982, year = {2025}, author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y}, title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {383}, pmid = {41052982}, issn = {2158-3188}, support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.}, } @article {pmid41052332, year = {2025}, author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C}, title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {41}, pages = {e2514823122}, doi = {10.1073/pnas.2514823122}, pmid = {41052332}, issn = {1091-6490}, support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; }, abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.}, } @article {pmid41050761, year = {2025}, author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X}, title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1631960}, pmid = {41050761}, issn = {2235-2988}, mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation & purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; }, abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.}, } @article {pmid41050671, year = {2025}, author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J}, title = {Microbial metabolites and their influence on the tumor microenvironment.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1675677}, pmid = {41050671}, issn = {1664-3224}, mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; }, abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.}, } @article {pmid41048389, year = {2025}, author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL}, title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20081}, pmid = {41048389}, issn = {2167-8359}, mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; }, abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.}, } @article {pmid41048034, year = {2025}, author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS}, title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70054}, doi = {10.1111/1755-0998.70054}, pmid = {41048034}, issn = {1755-0998}, abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.}, } @article {pmid41044998, year = {2025}, author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J}, title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.}, journal = {Microbial biotechnology}, volume = {18}, number = {10}, pages = {e70238}, pmid = {41044998}, issn = {1751-7915}, support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; }, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; }, abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.}, } @article {pmid40966609, year = {2025}, author = {Wu, L and Bao, D and Liao, H and Yan, M and Ge, Y and Han, Z and Xia, X}, title = {Pore-scale mass transfer heterogeneity shapes nutrient accessibility and functional assembly in porous microbial ecosystems.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf205}, pmid = {40966609}, issn = {1751-7370}, support = {2023YFF1103701//National Key Research and Development Program of China/ ; }, mesh = {*Ecosystem ; *Microbiota ; Porosity ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenomics ; Soil Microbiology ; Amino Acids/metabolism ; Biomass ; }, abstract = {Porous ecosystems represent ubiquitous microbial habitats across natural settings including soil, gut tract, and food matrices, where microscale spatial architecture critically shapes microbial colonization and interactions. Yet, the mechanisms of how pore-scale physical constraints influence microbial community assembly and metabolic performance remain poorly understood. Here, we employed a microfluidic platform with tunable inter-pillar spacings, coupled with a multi-omics approach including in situ imaging, exometabolomics, metagenomics, and metatranscriptomics, to investigate how pore-size modulates microbial community dynamics. Comparing representative small (50 μm) and large (150 μm) pore-sizes, we found that larger pore-sizes promoted greater biomass accumulation and significantly enhanced exometabolite production, particularly of amino acids. Microscopy and quantitative assays revealed that 150 μm pores facilitated more efficient substrate degradation, especially of carbohydrates. Taxonomic profiling showed that increasing pore-size reduced community evenness while enhancing richness, selectively enriching carbohydrate-degrading and amino acid-producing taxa, and promoting more complex, positively correlated co-occurrence networks. Metatranscriptomic analysis further demonstrated that larger pore-size significantly upregulated key functional genes involved in substrate degradation, amino acid biosynthesis, and stress response pathways. Fluorescent tracer assays revealed pronounced mass transfer heterogeneity, where smaller pores exhibited prolonged solute persistence and steeper chemical gradients, ultimately restricting substrate availability and microbial activity. Collectively, our results reveal that alleviation of microscale spatial constraints enhances nutrient accessibility, metabolic function, and community organization in porous ecosystems, underscoring the pivotal role of physical microstructure in regulating both the taxonomic composition and functional capacity of microbial ecosystems.}, } @article {pmid40848874, year = {2025}, author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J}, title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {49}, number = {8}, pages = {102675}, doi = {10.1016/j.clinre.2025.102675}, pmid = {40848874}, issn = {2210-741X}, mesh = {Humans ; *Appendicitis/microbiology/diagnosis/surgery ; Prospective Studies ; Male ; Adult ; Female ; *Rectum/microbiology ; *Microbiota ; Middle Aged ; Appendectomy ; Cohort Studies ; Aged ; Young Adult ; }, abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).}, } @article {pmid41044404, year = {2025}, author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL}, title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {34482}, pmid = {41044404}, issn = {2045-2322}, mesh = {*Fresh Water/microbiology ; Metagenome ; *Genome, Bacterial ; Genome Size ; Ecosystem ; *Bacteria/genetics/classification ; }, abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.}, } @article {pmid41044010, year = {2025}, author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L}, title = {The untapped potential of short-read sequencing in biodiversity research.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2025.09.001}, pmid = {41044010}, issn = {0168-9525}, abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.}, } @article {pmid41042593, year = {2025}, author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B}, title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.}, journal = {Microbial genomics}, volume = {11}, number = {10}, pages = {}, doi = {10.1099/mgen.0.001524}, pmid = {41042593}, issn = {2057-5858}, mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; }, abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.}, } @article {pmid41042396, year = {2025}, author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y}, title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {212}, pmid = {41042396}, issn = {1432-0614}, support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; }, mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; }, abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.}, } @article {pmid41039256, year = {2025}, author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y}, title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {607}, pmid = {41039256}, issn = {1471-2180}, support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; }, mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Metagenomics ; }, abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.}, } @article {pmid41039213, year = {2025}, author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J}, title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {612}, pmid = {41039213}, issn = {1471-2180}, support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; }, abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.}, } @article {pmid41039197, year = {2025}, author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI}, title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {601}, pmid = {41039197}, issn = {1471-2180}, support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; }, mesh = {*Soil Microbiology ; South Africa ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Metagenomics ; *Microbiota ; *Fabaceae/growth & development/microbiology ; Agriculture ; Farmers ; Biodiversity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tropical Climate ; Vigna/growth & development ; }, abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.

RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.

CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.}, } @article {pmid41037127, year = {2025}, author = {Arunrat, N and Mhuantong, W and Sereenonchai, S}, title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {102}, pmid = {41037127}, issn = {1432-184X}, support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; }, mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; }, abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.}, } @article {pmid41036626, year = {2025}, author = {Xia, Y and Liang, L and Wang, X and Chen, Z and Liu, J and Yang, Y and Xie, H and Ding, Z and Huang, X and Long, S and Wang, Z and Xu, X and Ding, C and Chen, Q and Feng, Q}, title = {MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.}, journal = {Nucleic acids research}, volume = {53}, number = {18}, pages = {}, doi = {10.1093/nar/gkaf954}, pmid = {41036626}, issn = {1362-4962}, support = {2022YFA1304100//National Key R&D Program of China/ ; 82 270 980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; 82 202 539//National Natural Science Foundation of China/ ; 2023ZD0501406//National Science and Technology Major Program/ ; 2019//National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; #202412A001//horizontal cooperation project with Shenzhen 01 Life Institute/ ; #202112E401//horizontal cooperation project with Shenzhen 01 Life Institute/ ; }, mesh = {*Metagenomics/methods ; Workflow ; *Software ; *Metagenome/genetics ; *Microbiota/genetics ; Humans ; }, abstract = {Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.}, } @article {pmid41035224, year = {2025}, author = {Farini, A and Strati, F and Molinaro, M and Mostosi, D and Saccone, S and Tripodi, L and Troisi, J and Landolfi, A and Amoroso, C and Cassani, B and Blanco-Míguez, A and Leonetti, E and Bazzani, D and Bolzan, M and Fortunato, F and Caprioli, F and Facciotti, F and Torrente, Y}, title = {Immunoproteasome Inhibition Positively Impacts the Gut-Muscle Axis in Duchenne Muscular Dystrophy.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {16}, number = {5}, pages = {e70054}, doi = {10.1002/jcsm.70054}, pmid = {41035224}, issn = {2190-6009}, support = {M6/C2_CALL 2022//PNRR/ ; FRRB-2022//Unmet Medical Needs, Fondazione Regionale per la Ricerca Biomedica/ ; GJC21084//Cariplo Telethon Alliance GJC2021-2022/ ; //NextGenerationEU/ ; //MUR/ ; PR-0394//Gruppo familiari beta-sarcoglicanopatie/ ; PNC-E3-2022-23683266-CUP: C43C22001630001//Hub Life Science-Diagnostica Avanzata/ ; //Associazione Centro Dino Ferrari/ ; }, mesh = {Animals ; *Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Proteasome Inhibitors/pharmacology/therapeutic use ; *Muscle, Skeletal/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred mdx ; Male ; *Proteasome Endopeptidase Complex/metabolism ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Duchenne Muscular Dystrophy (DMD) features immune-muscle crosstalk, where muscle fibre degeneration enhances pro-inflammatory macrophage infiltration, worsening inflammation and impairing regeneration.

METHODS: We investigated the impact of immunoproteasome (IP) inhibition on the gut-muscle axis in mdx mice, a well-established model of DMD. We employed microbiota perturbation models, including broad-spectrum antibiotic treatment (ABX) and faecal microbiota transplantation (FMT) from IP-inhibited mdx mice. IP inhibition effects were assessed by analysing gut microbiota composition, intestinal inflammation, muscle integrity and associated metabolic and inflammatory pathways.

RESULTS: IP inhibitor ONX-0914 significantly impacted the intestinal inflammatory microenvironment and gut microbiota of mdx mice. ONX-0914 treatment increased gastrointestinal transit (increased wet/dry faecal weights, p = 0.0486 and p = 0.0112, respectively) and partially restored intestinal barrier integrity (reduced FITC-dextran leakage, p = 0.0449). JAM-A was significantly upregulated (p < 0.0001). Colonic CD206+ M2 macrophages increased, while CD68 + M1 cells partially decreased. ONX-0914 downregulated IP isoforms in macrophages (PSMB8: p = 0.0022; PSMB9: p = 0.0186) as well as FOXO-1 (p = 0.0380) and TNF-α (p = 0.0487). Antibiotic-induced microbiota depletion abrogated these effects. Metagenomic analysis revealed significant differences in microbiota composition between C57Bl controls and mdx mice (PERMANOVA p < 0.001), with ONX-0914 inducing enrichment of stachyose degradation pathways. Metabolomic analysis showed enrichment of bacterial metabolites, fatty acid and sugar metabolism pathways, with increased glutathione, galactose, glycerol, glyceraldehyde and TCA cycle intermediates. ONX-0914 improved mitochondrial activity in skeletal muscle, as increased expression of ETC complexes (mdx vs. mdx+ONX: Complex II, p = 0.0338; Complex IV, p = 0.0023) and TCA enzymes (mdx vs. FTMmdx+ONX: IDH p = 0.0258; FH p = 0.0366). This led to a shift towards oxidative muscle fibres and improved muscle morphology (increased fibre size, p < 0.0001 mdx vs. mdx+ONX and mdx vs. FTMmdx+ONX). Muscle performance was enhanced with reduced CPK levels (p = 0.0015 mdx vs. mdx+ONX) and fibrosis (decreased TGFβ: mdx vs. mdx+ONX, p = 0.0248; mdx vs. FTMmdx+ONX, p = 0.0279). ONX-0914 reduced CD68+ (mdx vs. mdx+ONX, p = 0.0024; mdx vs. FTMmdx+ONX, p < 0.0001) and increased CD206+ (mdx vs. FTMmdx+ONX: p = 0.0083) macrophages in muscle, downregulated inflammatory genes (mdx vs. mdx+ONX: ccl2 p = 0.0327, vcam-1p = 0.0378) and reduced pro-inflammatory proteins (MCP1, mdx vs. mdx+ONX, p = 0.0442). Inflammatory cytokines and endothelial vessel density in ONX-0914 treated mdx were restored to wild type mice. These data demonstrate that ONX-0914 enhances muscle function through microbiota-dependent mechanisms.

CONCLUSIONS: Our study advances the understanding of the role of dysbiosis in DMD disease and identifies IP inhibition as a potential therapeutic strategy to modulate the dystrophic gut-muscle axis, offering new perspectives for microbiota-targeted therapies.}, } @article {pmid41034963, year = {2025}, author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL}, title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {199}, pmid = {41034963}, issn = {2049-2618}, support = {Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; DBI 20222070//National Science Foundation/ ; 1K08ES034821-01A1/NH/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.

RESULTS: In relation to urine sample volume, ≥ 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.

CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.}, } @article {pmid41030387, year = {2025}, author = {Zheng-Qiang, L and Jun, L and Rui, A and Rui, L and Wei, D and Ping, M and Xu, Y and Rong, S and Xiao-Yan, Y and Wen, X}, title = {A probiotic for preventing microplastic toxicity: Clostridium dalinum mitigates microplastic-induced damage via microbiota-metabolism-barrier interactions.}, journal = {Current research in food science}, volume = {11}, number = {}, pages = {101200}, pmid = {41030387}, issn = {2665-9271}, abstract = {Microplastics (MPs) are widely distributed and accumulated in the environment, making it nearly impossible for humans to avoid ingestion. Their toxicity can cause serious health damage and pose a threat to human health. In this context, developing strategies to prevent and restore toxic damage from their ingestion is extremely urgent. This study comprehensively employs various techniques, including metagenomics and metabolomics, to explore the pre-protective and restorative effects of Clostridium dalinum, a potential probiotic with excellent antioxidant and anti-inflammatory capabilities, on damage induced by exposure to polystyrene microplastics (PS-MPs) in mice. The results show that exposure to PS-MPs leads to significant intestinal damage in mice; preemptive intake of C. dalinum for pre-protection, or post-exposure intake of C. dalinum for restorative treatment, both significantly reduced the damage caused by MPs exposure, as evidenced by changes in intestinal length (PS-MPs exposure vs C. dalinum pre-protection vs C. dalinum restoration vs control = 36.55 vs 39.94 vs 40.12 vs 41.05 cm), barrier protein content (27.12 % vs 97.28 % vs 97.73 % vs 100.00 %), and inflammation levels (284.56 % vs 101.05 % vs 98.17 % vs 100.00 %). Mechanistically, the pre-protective and restorative effects of C. dalinum both rely on upregulating the expression of barrier proteins such as ZO-1 and Occludin and inhibiting the TLR4/NF-κB inflammatory signaling pathway. Meanwhile, the two intervention modes also exhibit specific mechanisms: in the pre-protection mode, C. dalinum enhances lipid metabolic balance and antioxidant reserves by pre-activating the PPARγ/GPR43 pathway, and enriches the ABC transporters pathway to promote toxin efflux capacity, thereby preventing PS-MPs-induced damage; in the restoration mode, C. dalinum repairs intestinal damage by enriching the beneficial bacterium Lachnospiraceae NK4A136 and inhibiting the pro-inflammatory bacterium Desulfovibrio, and regulating intestinal metabolites. In summary, this study is the first to confirm that C. dalinum can effectively prevent and restore intestinal damage caused by PS-MPs exposure through the synergistic pathway of "microbiota-metabolism-barrier". Importantly, this study is the first to reveal the potential and unique mechanisms of probiotics in preventing and restoring MPs exposure toxicity, providing a theoretical basis for the future development of probiotic-based defense strategies.}, } @article {pmid41006832, year = {2025}, author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ}, title = {A roadmap for equitable reuse of public microbiome data.}, journal = {Nature microbiology}, volume = {10}, number = {10}, pages = {2384-2395}, pmid = {41006832}, issn = {2058-5276}, support = {CTC 1439/2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; MO3498/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OCE-2049445//National Science Foundation (NSF)/ ; }, mesh = {*Microbiota/genetics ; *Information Dissemination/methods ; Humans ; }, abstract = {Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates that the data creators prefer to be contacted before data reuse, and simultaneously provides data consumers with a mechanism to get in touch with the data creators. The DRI aims to facilitate and foster collaborations, and serve as a guideline that can be expanded to other data types.}, } @article {pmid40987851, year = {2025}, author = {Du, LF and Shi, W and Cui, XM and Fan, H and Jiang, JF and Bian, C and Ye, RZ and Wang, Q and Zhang, MZ and Yuan, TT and Xia, LY and Ruan, XD and Chang, QC and Du, CH and Que, TC and Wang, X and Han, XH and Yang, TC and Jiang, BG and Chen, JY and Wang, XR and Tan, LF and Liu, YW and Deng, LL and Liu, Y and Zhu, Y and Pan, YS and Wang, N and Lin, ZT and Li, LF and Li, C and Shen, SJ and Liu, YT and Tian, D and Han, XY and Wang, J and Wang, YF and Gao, WY and Li, YY and Xiong, T and Wang, TH and Shi, XY and Zhu, DY and Zhu, JG and Wang, CC and Shi, WQ and Zhan, L and Liu, ZH and Feng, D and Zhao, L and Sun, Y and , and Wang, J and Jia, N and Zhao, F and Cao, WC}, title = {Genome-resolved metagenomics reveals microbiome diversity across 48 tick species.}, journal = {Nature microbiology}, volume = {10}, number = {10}, pages = {2631-2645}, pmid = {40987851}, issn = {2058-5276}, support = {2019YFC1200501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025009//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Ticks/microbiology/classification/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; China ; Symbiosis ; Tick-Borne Diseases ; Genome-Wide Association Study ; Host Microbial Interactions/genetics ; Host-Pathogen Interactions/genetics ; }, abstract = {Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host-microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.}, } @article {pmid40935925, year = {2025}, author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y}, title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.}, journal = {Nature microbiology}, volume = {10}, number = {10}, pages = {2396-2411}, pmid = {40935925}, issn = {2058-5276}, support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Phenazines/metabolism/pharmacology ; Rhizosphere ; *Microbiota/drug effects ; Bacillus subtilis/drug effects/genetics/enzymology ; *DNA Topoisomerase IV/metabolism/antagonists & inhibitors/genetics ; Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; *Bacteria/genetics/classification/metabolism/drug effects ; Fusarium/drug effects ; Pseudomonas/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Genome, Bacterial ; DNA Damage/drug effects ; Metagenomics ; }, abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.}, } @article {pmid40921745, year = {2025}, author = {Zhang, X and Li, Y and Qin, Y and Liao, Z and Deng, C and Chen, Y and Li, Y and Qian, H and He, Y and Chen, S and Shi, G and Liu, Y}, title = {Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren's disease.}, journal = {Nature microbiology}, volume = {10}, number = {10}, pages = {2591-2602}, pmid = {40921745}, issn = {2058-5276}, support = {82471833//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101841//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171779//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82371802//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023J06055//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; 2022XMSLCYX01//Xiamen Municipal Bureau of Science and Technology (Xiamen Science and Technology Bureau)/ ; }, mesh = {*Capsid Proteins/immunology/genetics ; *Sjogren's Syndrome/immunology/virology ; Humans ; *Autoantigens/immunology ; *Molecular Mimicry/immunology ; Animals ; Mice ; Female ; *Autoimmunity ; Saliva/virology ; Autoantibodies/immunology/blood ; Middle Aged ; Male ; Adult ; Virome ; }, abstract = {Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren's disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion of Siphoviridae bacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry.}, } @article {pmid40819273, year = {2025}, author = {Puranik, S and Mekali, J and Damodaram, KJP}, title = {Seed Biopriming From Basics to Omics: Relieving Plants From Biotic Stress Through the Microbial Way.}, journal = {Journal of basic microbiology}, volume = {65}, number = {10}, pages = {e70083}, doi = {10.1002/jobm.70083}, pmid = {40819273}, issn = {1521-4028}, mesh = {*Seeds/microbiology/growth & development ; *Stress, Physiological ; *Crops, Agricultural/microbiology/growth & development ; Plant Diseases/prevention & control/microbiology ; Rhizosphere ; Animals ; Metabolomics ; Proteomics ; Microbiota ; Plant Development ; *Agricultural Inoculants/physiology ; Metagenomics ; Plant Growth Regulators/metabolism ; }, abstract = {From seed to harvest, cultivated crops face numerous biotic stresses, including insects, nematodes, and diseases, which significantly hinder their growth and vigor, resulting in substantial crop losses. In contrast to use of toxic agrochemicals, seed biopriming with microbial inoculants has emerged as an effective and eco-friendly alternative against pathogens and pests. Seed biopriming involves coating seeds with beneficial microorganisms that enhance protection and immunity against a variety of harmful pests and pathogens. These microbial agents colonize the seeds and establish themselves in the rhizosphere, reducing the impact of biotic stresses while fostering a healthier environment for plant growth. They are known to exhibit several mechanisms against pathogens and pests, like production of cell wall degrading enzymes, antibiosis, competition, induced systemic resistance, chelation of iron etc. Additionally, these microorganisms regulate phytohormone levels, further optimizing the physiological and metabolic characteristics of plants. This approach not only promotes robust plant growth but also enhances tolerance to deleterious bacteria, fungi, nematodes and arthropods, ensuring healthier crops. These interactions can further be well studied and expressed by using different omics approaches like metagenomics (of seed microbiome), proteomics, transcriptomics, metabolomics and differential gene expression. This review highlights the role and benefits of seed biopriming as a sustainable strategy to manage biotic stresses effectively, and the importance of omics for better understanding of complex processes during such interactions, contributing to resilient agricultural production systems and environmental sustainability.}, } @article {pmid41029845, year = {2025}, author = {Rey-Velasco, X and Auladell, A and Deulofeu-Capo, O and Lundin, D and Pinhassi, J and Ferrera, I and Sánchez, O and Gasol, JM}, title = {Decoding the genetic drivers of marine bacterial blooms through comparative genomics.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {198}, pmid = {41029845}, issn = {2049-2618}, support = {PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; FPU20/01625//Ministerio de Universidades/ ; }, mesh = {*Bacteria/genetics/classification/growth & development/isolation & purification ; *Genome, Bacterial ; *Seawater/microbiology ; *Genomics/methods ; *Microbiota/genetics ; Phytoplankton ; Metagenome ; Eutrophication ; Metagenomics/methods ; }, abstract = {BACKGROUND: While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.

RESULTS: We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.

CONCLUSIONS: In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.}, } @article {pmid41029787, year = {2025}, author = {Lemieux, É and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, É and Fournaise, S and Vincent, AT}, title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {402}, pmid = {41029787}, issn = {1756-0500}, support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; }, abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.

RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both α- and β-diversity between sample types (digesta, feces) than between treatments. β-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. β-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.}, } @article {pmid41028378, year = {2026}, author = {Sahil, R and Jain, M}, title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2977}, number = {}, pages = {181-196}, pmid = {41028378}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; }, abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.}, } @article {pmid41026172, year = {2025}, author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y}, title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {98}, pmid = {41026172}, issn = {1432-184X}, support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; }, abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.}, } @article {pmid40958146, year = {2025}, author = {Yang, Q and Liu, J and Lyu, S and Li, S and Han, Q and Ma, C and Du, Z and Zhang, T}, title = {Ovalbumin Peptides Restore Intestinal Barrier Integrity via Gut-Liver Axis Modulation of Bile Salt Hydrolase and Bile Acids Crosstalk.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {39}, pages = {24741-24752}, doi = {10.1021/acs.jafc.5c07236}, pmid = {40958146}, issn = {1520-5118}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Ovalbumin/chemistry/administration & dosage ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Male ; *Amidohydrolases/metabolism/genetics ; Humans ; *Intestinal Mucosa/metabolism/drug effects ; *Peptides/administration & dosage/chemistry ; *Colitis/metabolism/drug therapy/microbiology/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fibroblast Growth Factors/metabolism/genetics ; *Inflammatory Bowel Diseases/metabolism/drug therapy/microbiology/genetics ; Mucin-2/genetics/metabolism ; Tumor Necrosis Factor-alpha/genetics/metabolism ; }, abstract = {Inflammatory bowel disease (IBD) is characterized by intestinal barrier dysfunction and bile acid (BA) dysmetabolism. BA metabolism was a pivotal regulator in the "gut-liver axis" to maintain intestinal homeostasis. Ovalbumin-derived peptides (OVA-Ps) exhibit potential in barrier repair; however, their systemic mechanisms within the microbiota-BA-host network remain underexplored. This study investigates the therapeutic potential of the oligomer OVA-P in a DSS-induced colitis mouse model. OVA-P administration significantly alleviated colitis symptoms, restored colon length, reduced pro-inflammatory cytokines (tumor necrosis factor-α), and enhanced antioxidant markers (SOD). Mechanistically, the OVA-P reshaped gut microbiota composition, suppressed bile salt hydrolase (BSH), and elevated conjugated BAs (e.g., taurocholic acid) levels. These changes activated the farnesoid X receptor (FXR) pathway, upregulating tight junction protein (ZO-1), and mucin (MUC-2) expression, thereby restoring intestinal barrier integrity. Metabolomic and metagenomic analyses confirmed the OVA-P-mediated modulation of the gut-liver axis through FXR-SHP/FGF15 signaling, highlighting its role in maintaining BA homeostasis. These findings provide insights into the use of OVA-P as a dietary intervention for IBD by targeting microbiota-BA-FXR interactions, offering a foundation for high-value egg protein applications in functional foods.}, } @article {pmid40925130, year = {2025}, author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ}, title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {392}, number = {9}, pages = {103659}, doi = {10.1016/j.jpet.2025.103659}, pmid = {40925130}, issn = {1521-0103}, mesh = {*Lupus Erythematosus, Systemic/microbiology/immunology/therapy/drug therapy ; Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation/methods ; Dysbiosis/immunology ; }, abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.}, } @article {pmid40794770, year = {2025}, author = {Chia, M and Pop, M and Salzberg, SL and Nagarajan, N}, title = {Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.}, journal = {Cancer research}, volume = {85}, number = {19}, pages = {3584-3595}, pmid = {40794770}, issn = {1538-7445}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; OFYIRG21nov-0024//National Medical Research Council (NMRC)/ ; R35-GM130151//National Institute of General Medical Sciences (NIGMS)/ ; R01-HG006677//National Human Genome Research Institute (NHGRI)/ ; NRFI09-0015//National Research Foundation Singapore (NRF)/ ; }, mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; }, abstract = {The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research holds promise for identifying noninvasive biomarkers and possibly new paradigms for cancer treatment. In this review, we explore the key computational challenges and opportunities in analyzing cancer-associated microbiomes (in tumor/normal tissues and other body sites, e.g., gut, oral, and skin), focusing on sequencing-driven strategies and associated considerations for taxonomic and functional characterization. The discussion covers the strengths and limitations of current analysis tools for identifying contamination, determining compositional bias, and resolving species and strains, as well as the statistical, metabolic, and network inferences that are essential to uncover host-microbiome interactions. Several key considerations are required to guide the choice of databases used for metagenomic analysis in such studies. Recent advances in spatial and single-cell technologies have provided insights into cancer-associated microbiomes, and Artificial Intelligence-driven protein function prediction might enable rapid advances in this field. Finally, we provide a perspective on how the field can evolve to manage the ever-growing size of datasets and generate robust and testable hypotheses. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .}, } @article {pmid41026152, year = {2025}, author = {Nassirnia, S and Scherz, V and Greub, G and Caruana, G and Taffé, P and Jaton, K and Papis, S and Posfay-Barbe, KM and Mornand, A and Rochat-Guignard, I and Bertelli, C and Asner, SA}, title = {Concordance between upper and lower airway microbiota in children with cystic fibrosis.}, journal = {Journal of medical microbiology}, volume = {74}, number = {9}, pages = {}, doi = {10.1099/jmm.0.002079}, pmid = {41026152}, issn = {1473-5644}, mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Adolescent ; Longitudinal Studies ; *Respiratory System/microbiology ; Metagenomics ; Infant ; }, abstract = {Introduction. Sputum is the most used sample type to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate.Hypothesis. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.Aim. We aimed to compare bacterial community diversity and composition between sputum and throat swabs in the full cohort and in patients with paired samples from the same visit.Methodology. The prospective longitudinal multicentre MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.Results. Sputum and throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen's kappa: 0.6). Differences in bacterial abundance were observed (P=0.001), but not presence/absence (P=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swab microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (adjusted Rand index=0.08 and 0.10). The average beta-diversity distances between samples collected from the same visit were shorter (0.505±0.056 95% confidence interval), compared with sputum (0.695±0.017) or throat swab (0.704±0.045) from the same patient collected during different visits.Conclusion. Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.}, } @article {pmid41025248, year = {2025}, author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK}, title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {9}, pages = {e2507003}, doi = {10.71150/jm.2507003}, pmid = {41025248}, issn = {1976-3794}, support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; }, mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; }, abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.}, } @article {pmid41024767, year = {2025}, author = {Ezzat, WM}, title = {Machine learning as an artificial intelligence application in management of chronic hepatitis B virus infection.}, journal = {World journal of gastroenterology}, volume = {31}, number = {35}, pages = {109776}, pmid = {41024767}, issn = {2219-2840}, mesh = {Humans ; *Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Hepatitis B virus/pathogenicity ; Algorithms ; Artificial Intelligence ; Antiviral Agents/therapeutic use ; Supervised Machine Learning ; }, abstract = {Let's review the role of gut microbiota in pathogenesis of chronic hepatitis B infection as addressed in by Zhu et al. Zhu et al used high-throughput technology to characterize the microbial ecosystems, which led to an explosion of various types of molecular profiling data, such as metagenomics, metatranscriptomics, and metabolomics. To analyze such data, machine learning (ML) algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and, particularly, for generating models that can accurately predict phenotypes. Strong evidence suggests that such gut microbiome-based stratification could guide customized interventions to benefit human health. Supervised learning includes designing an algorithm to fix a pre-identified problem. To get an answer, ML software must access data that have been nominated. On the other hand, unsupervised learning does not address any pre-defined problems. Bias should be eliminated as much as possible. In unsupervised learning, an ML algorithm works to identify data patterns without any prior operator input. This can subsequently lead to elements being identified that could not be conceived by the operator. At the intersection between supervised and unsupervised learning is semi-supervised ML. Semi-supervised learning includes using a partially labeled data set. The ML algorithm utilizes unsupervised learning to label data (that has not yet been labelled) by drawing findings from the labeled data. Then, supervised techniques can be used to solve defined problems involving the labeled data. Reinforcement learning, which is similar to supervised learning in the meaning, is goal-oriented. Reinforcement learning does not need labeled data, instead, it is provided with a set of regulations on a problem. An algorithm will carry out operations to try to answer questions involving the problem. Based on obtained data of gut microbiota, various therapeutic modalities can be applied: Prebiotics, probiotics, postbiotics, engineered bacteria, bacteriophage, and novel microbe-materials therapeutic system and fecal transplantation. In conclusion, ML is an artificial intelligence application that helps in providing new perspectives on tailored therapy. Furthermore, assessing the impact of gut microbiota modification is a critical step in advanced liver disease management. These new artificial intelligence techniques although promising, still require further analysis and validation in future studies.}, } @article {pmid41024212, year = {2025}, author = {Wang, Y and Gong, L and Dong, D and Li, X}, title = {Metagenomic binning reveals community and functional characteristics of sulfur- and methane-oxidizing bacteria in cold seep sponge ground.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {122}, pmid = {41024212}, issn = {2524-6372}, support = {KEXUE2020GZ01//The Senior User Project of R/V Kexue/ ; 42176114//The National Natural Science Foundation of China/ ; ZR2023MD100//Natural Science Foundation of Shandong Province/ ; }, abstract = {BACKGROUND: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.

RESULTS: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.

CONCLUSIONS: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.}, } @article {pmid41023790, year = {2025}, author = {Cao, L and Sun, H and Wang, Y and Wei, Z and Zhang, J and Wang, Y and Yan, J and Zhu, Y and Cheng, N and He, S and Liu, X and Li, T and Wang, M and Li, E}, title = {Comparative analysis of metagenomics between high- and medium-temperature daqu, and microbial succession in Jiang-Nong Jianxiang Baijiu fermentation.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {852}, pmid = {41023790}, issn = {1471-2164}, mesh = {*Fermentation ; *Metagenomics/methods ; *Alcoholic Beverages/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Temperature ; Phylogeny ; }, abstract = {BACKGROUND: The mixture of high-temperature Daqu and medium-temperature Daqu can be used to produce Chinese Jiang-Nong Jianxiang Baijiu. This study used metagenomic sequencing and physicochemical analysis to investigate the microbial community and functionality of high-temperature Daqu and medium-temperature Daqu. In addition, exploring the changes of microbial communities during the Jiang-Nong Jianxiang Baijiu fermentation process.

RESULTS: The results showed that Lichtheimia ramose and Saccharopolyspora rectivirgula were the significantly different species in high-temperature Daqu. However, Paecilomyces variotii, Aspergillus chevalieri, and Rasamsonia emersonii were the significantly different species in medium-temperature Daqu. The medium-temperature Daqu had higher saccharifying power (101.20 ± 1.85 U/g) than high-temperature Daqu (60.00 ± 0.58 U/g). And the protease activity of high-temperature Daqu (62.47 ± 5.84 U/mg) was significantly higher than medium-temperature Daqu (36.10 ± 1.13 U/mg). The community structure analysis results of the stack fermentation stage showed that the mixture of high-temperature Daqu and medium-temperature Daqu inherited the community advantages of both high-temperature Daqu and medium-temperature Daqu. With Jiang-Nong Jianxiang Baijiu fermentation, the significantly different species changed from Pichia sp., Acetobacter sp., and Lactobacillus sp. to Pediococcus sp., Lactobacillus sp., Lentilactobacillus sp., Saccharomyces sp., Thermoactinomyces sp., and Saccharopolyspora sp., implying the importance of acid-resistant and ethanol-resistant microorganisms for the production of flavor substances in the late Baijiu fermentation.

CONCLUSIONS: Our research revealed the difference in microbial communities between high-temperature Daqu and medium-temperature Daqu, and demonstrated the shifts and functionality of microbiota during Jiang-Nong Jianxiang Baijiu fermentation. This study provides a theoretical reference for utilizing core synergistic microbiota and their functional traits in Baijiu fermentation starters to improve Baijiu quality.}, } @article {pmid41023192, year = {2025}, author = {Vishal, V and Thakur, P and Tigga, SS and Lal, S}, title = {A metagenomic assessment of overburden dump of coal mine soil bacterial consortium from Jharkhand, India.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {10}, pages = {1161}, pmid = {41023192}, issn = {1573-2959}, mesh = {*Soil Microbiology ; India ; *Bacteria/classification/genetics ; *Coal Mining ; *Environmental Monitoring ; *Soil Pollutants/analysis ; Metagenomics ; Soil/chemistry ; *Microbial Consortia ; Biodegradation, Environmental ; RNA, Ribosomal, 16S ; Coal ; }, abstract = {Overburden dump (OBD) of coal mine waste soils is arguably a major source of heavy metals and metalloids, leading to both public health and ecological consequences. This study employed hypervariable V3-V4 region of 1.5 kbp 16S rDNA gene-based amplicon metagenomic sequencing to analyze unexplored bacterial diversity and its phenotypical and hypothetical functions, emphasizing the significance of these studies for assessing the potential of bioremediation. Triplicate coal OBD soil samples were collected from the coal dumping yard of Sarubera Colliery from Atna-Chainpur and agricultural soils from Ramgarh Cantonment, Jharkhand. There were 30 phyla And 320 operational taxonomic units (OTUs) recorded in coal OBD soil, while agricultural soil had 26 phyla And 240 OTUs. Proteobacteria were the predominant phylum in both environments. Firmicutes, Actinobacteria, and Bacteroidetes were the most prevalent phyla in the coal OBD soil, whereas Acidobacteria, Planctomycetes, and Nitrospirae were most frequently found in agricultural soil. Alphaproteobacteria and Gammaproteobacteria was the most abundant classes, and whereas the mesophilic Acinetobacter were the most abundant genus detected in coal OBD soil. The PICRUSt2 pipeline predicted hypothetical functional categories, identifying 2404 EC numbers, 7813 KO terms, And 442 MetaCyc pathways. The most enriched categories were RNA polymerase sigma-70 factor, ABC transporters, And 3-oxoacyl-[acyl-carrier-protein] reductase, aerobic respiration pathways, and pyruvate fermentation biosynthesis pathways. Taxonomy-to-phenotypic mapping was used to record phenotypic categories like oxygen requirement, temperature range, energy sources, biotic relationships, and Gram stain nature between the two habitats. The presence of nitrogen-fixing and phosphate-solubilizing bacteria in coal OBD soil offers their key roles of biodegrading polycyclic aromatic hydrocarbons (PAHs), speeding mineralization, and ameliorating environmental issues that threaten plant viability.}, } @article {pmid41022942, year = {2025}, author = {Halifu, S and Deng, X and Yang, L and Qian, L and Yang, L}, title = {Metagenomic analysis of pathogenicity of puccinia xanthii on invasive plant xanthium italicum.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33530}, pmid = {41022942}, issn = {2045-2322}, support = {KX031042//PhD research startup foundation of Shihezi University/ ; KX6107//a program of Shihezi University/ ; }, mesh = {*Plant Diseases/microbiology ; Plant Leaves/microbiology ; *Xanthium/microbiology ; *Metagenomics/methods ; *Puccinia/genetics/pathogenicity ; Introduced Species ; Photosynthesis ; China ; }, abstract = {Biological invasion refers to the establishment and proliferation of non-indigenous species in previously unoccupied areas, where they form wild populations. Xanthium italicum, an invasive species in Xinjiang, China, negatively affects local ecosystems, agriculture, and animal husbandry. In this study, we investigated the pathogenicity of Puccinia xanthii on the leaves of X. italicum by exploring the morphological characteristics of the pathogenic fungi, leaf enzyme activity measurement, photosynthesis measurement, and metagenomic sequencing. This study showed that P. xanthii infects the leaves of X. italicum, significantly reducing the activities of lyase, oxidoreductase, and antioxidant enzymes, including phenylalanine ammonia-lyase (PAL), superoxide dismutase (SOD), polyphenol oxidase (PPO), and catalase (CAT), as well as impairing photosynthesis. Furthermore, metagenomic analysis indicated that P. xanthii infection reduced the homogeneity and richness of phyllosphere microorganisms and increased the abundance of P. xanthii in the phyllosphere. Functional analysis also revealed that P. xanthii infection altered the diversity of microbial functions and eventually led to the development of disease symptoms and the demise of leaves through activated oxidative phosphorylation.}, } @article {pmid41022706, year = {2025}, author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE}, title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8559}, pmid = {41022706}, issn = {2041-1723}, support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; }, mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; }, abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.}, } @article {pmid41021050, year = {2025}, author = {Kishk, M and Rahmeh, R and Asiri, F and Karam, H and Al-Muhanna, K and Hejji, AB and Shajan, A and Al-Salem, SM}, title = {Substrate-specific microbial community shifts during mesophilic biodegradation of polymers in compost amended soil.}, journal = {Biodegradation}, volume = {36}, number = {5}, pages = {93}, pmid = {41021050}, issn = {1572-9729}, support = {FB187K//Kuwait Institute for Scientific Research/ ; }, mesh = {Biodegradation, Environmental ; *Soil Microbiology ; *Soil/chemistry ; *Polymers/metabolism ; *Composting ; *Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fungi/metabolism/genetics/classification ; Starch/metabolism ; }, abstract = {Plastics are widely utilized across various industries, but their persistent accumulation in the environment has become a major ecological concern. Biodegradable alternatives offer a potential solution to plastic pollution; however, their degradation behavior under environmentally relevant conditions remains underexplored. This study evaluates the aerobic biodegradation of four polymer materials: starch, commercial thermoplastic starch of polyester origin (TPS1), linear low-density polyethylene (LLDPE), and a co-polyester thermoplastic starch (TPS2), over 180 days at 25 °C in a compost-soil matrix using the testing protocols of ASTM D5988-18 for carbon dioxide (CO2) evolution. Microbial community dynamics were profiled using 16S rRNA and ITS2 amplicon sequencing. TPS2 reached complete mineralization (~ 100%) in 28 days, followed by starch at 71.1% by day 180. TPS1 showed partial mineralization of 38.6%, while LLDPE showed minimal mineralization (21.9%) as expected. Alpha diversity revealed higher bacterial richness in starch treatments and a marked reduction in fungal diversity in TPS1 and LLDPE. Differential abundance testing revealed significant microbial shifts between treatments. Linear discriminant analysis Effect Size (LEfSe) identified polymer-specific microbial biomarkers, including Paenibacillus and Botryotrichum for starch, Acrophialophora and Mycothermus for TPS2, and the Mycobacterium for LLDPE. Subgroup 10 Acidobacteria was uniquely enriched in TPS2-treated samples. These taxa reflect substrate-driven microbial selection. Coupling CO2 mineralization with microbial profiling offers a practical framework to evaluate polymer biodegradability and guide the design of soil-degradable bioplastics. Overall, these findings demonstrate that polymer composition significantly influences microbial community structure and mineralization performance under mesophilic conditions.}, } @article {pmid40940575, year = {2025}, author = {Abenaim, L and Mercati, D and Mandoli, A and Carpentier, J and Noël, G and Conti, B and Caparros Megido, R and Dallai, R}, title = {Exploring the plastivorous activity of Hermetia illucens (Diptera Stratiomyidae) larvae.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {36}, pages = {21649-21665}, pmid = {40940575}, issn = {1614-7499}, mesh = {Animals ; Larva ; *Diptera ; Biodegradation, Environmental ; Gastrointestinal Microbiome ; }, abstract = {Hermetia illucens (Diptera Stratiomyidae), also known as Black Soldier Fly (BSF), is one of the insect species most investigated for biodegradation ability in its larvae. H. illucens larvae can biodegrade organic waste but also contaminants like pesticides, antibiotics, and mycotoxins. This study wants to investigate the ability of these larvae to degrade polystyrene (PS). Experiments evaluated the growth performance, survival rates, intestinal and intracellular morphological alterations, degradation by-product formation and intestinal microbiota alterations of larvae fed a PS-enriched diet. Despite the addition of PS microparticles, no significant differences in growth or survival were observed compared to the standard diet (p > 0.05). Confocal Laser Scanning Microscopy and Transmission Electron Microscopy confirmed the presence of PS microparticles in the larval gut, with potential signs of biodegradation. Metabolomic analyses identified styrene in the gut after 1 and 3 days of PS feeding, but its occurrence was likely due to thermal depolymerisation of the PS microparticles under GC-MS conditions. Metagenomic analysis revealed significant shifts in the intestinal microbiota. Notably, an enrichment of Corynebacterium, known for its role in aerobic PS degradation, and the abundance increase of other genera (Enterococcus, Enterobacteriaceae, Enterobacter, and Escherichia-Shigella) associated with synthetic polymer metabolism was observed. These results confirm the potential of BSF larvae to manage plastic waste through the interaction between their gut microbiota and synthetic materials. This study provides a foundation for future research focusing on isolating bacterial communities and enzymatic processes involved in polymer degradation, aiming to develop sustainable strategies for plastic waste management.}, } @article {pmid40784060, year = {2025}, author = {Zhang, H and Wang, C and Gong, Y and Zhu, Y and Zhang, M and Li, D and Tian, Y and Han, R and Guo, Y and Zhang, Y and Kang, X and Jiang, R}, title = {Changes in pathogenicity of gut microbiota during fasting-induced molting in laying hens and their impact on spleen immune function.}, journal = {Poultry science}, volume = {104}, number = {10}, pages = {105526}, pmid = {40784060}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/immunology/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; *Molting ; *Spleen/immunology ; Random Allocation ; *Fasting ; Food Deprivation ; }, abstract = {Fasting-induced molting (FIM) leverages the natural molting mechanism of aging laying hens to enhance their egg production and egg quality. However, fasting may also increase the risk of pathogen infection and activate immune regulation in the spleen. Understanding the specific types of pathogen infections triggered during FIM and their impacts on the spleen's immune regulation mechanisms is crucial for enhancing the immunological resilience of poultry. A total of 90, aged 60 weeks, late-laying hens were randomly assigned to undergo FIM. During FIM, hens kept regular feed and 16 hours light initially. A 3-day fast with 8 hours light followed. Then, they gradually resumed water and feed, increasing from 30 g to 120 g daily, with light returning to 16 hours. This study investigates the effects of FIM on the gut microbiota and metabolites through metagenomic sequencing and metabolomics. Additionally, blood routine tests and ELISA assays were conducted to measure serum Ig concentrations. Real-time quantitative PCR and ELISA were used to detect the expression of inflammatory factors and immune cell markers in the spleen. The study also analyzed gene expression levels in the PI3K/AKT pathway, systematically exploring fasting's regulatory impact on gut-spleen immunity. Results showed that during FIM, the abundance of pathogens utilizing non-carbohydrates as an energy source initially increased and then decreased, while the abundance of pathogens relying on carbohydrates as an energy source declined. Correspondingly, with beneficial metabolites initially decreased before increasing, while harmful metabolites exhibited the opposite trend. During fasting, the concentration of eosinophilic leukocytes in serum significantly increased (P < 0.05), while the concentration of IgA significantly decreased (P < 0.05). In the spleen, significant increase in the expression of immune-related metabolites, including NF-κB, IFN-β, iNOS, IL-1β, and IFN-α, were observed, along with significant increases in the secretion of TNF-α, TGF-β, IL-1, and IL-8, suggesting a significant activation of the immune response. After refeeding, these factors in serum and spleen returned to pre-fasting levels. Notably, the PI3K/AKT signaling pathway was significantly activated during fasting, indicating that fasting exerts broad effects on the immune system via the PI3K/AKT pathway. This study holds significant theoretical and practical value for enhancing the immunity of molting laying hens, reducing pathogenic bacterial infections, and optimizing production performance.}, } @article {pmid40715695, year = {2025}, author = {Yu, L and Guo, Q and Gu, X and Wang, Z and Li, J and Wang, X and Xu, Z and Wang, Y and Zhang, Y and Zhang, Y and Ding, Y and Chen, Z and Chen, K and Ding, Y}, title = {Impact of gut microbiome on radiotherapy and immunotherapy efficacy in microsatellite-stable colorectal cancer: role of propionic acid and B. fragilis.}, journal = {British journal of cancer}, volume = {133}, number = {7}, pages = {956-969}, pmid = {40715695}, issn = {1532-1827}, mesh = {*Colorectal Neoplasms/therapy/microbiology/immunology/genetics/pathology ; *Gastrointestinal Microbiome/immunology/drug effects ; Animals ; Mice ; *Immunotherapy/methods ; *Propionates/metabolism/pharmacology ; Microsatellite Instability ; *Bacteroides fragilis ; Humans ; Tumor Microenvironment/immunology ; Female ; CD8-Positive T-Lymphocytes/immunology ; Combined Modality Therapy ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths worldwide. While immunotherapy is effective in microsatellite instability-high (MSI-H) CRC, its benefits in microsatellite-stable (MSS) CRC are limited. Radiotherapy may modify the immune microenvironment in MSS-CRC, enhancing immunotherapy efficacy, but individual responses vary.

METHODS: We employed MSS-CRC mouse models to examine the effects of combined radiotherapy and immunotherapy, with and without antibiotics (ABX). Various analyses, including metagenomic, nontargeted metabolomic, and gas chromatography-mass spectrometry (GC-MS), were performed to identify factors influencing treatment outcomes. Flow cytometry, immunohistochemistry and in vivo antibody blockade experiments assessed the role of metabolites and bacteria on CD8[+] T cell infiltration and treatment responses, complemented by transcriptomic sequencing and molecular biology experiments.

RESULTS: Our analyses identified propionic acid and Bacteroides fragilis (B. fragilis) as crucial factors enhancing the efficacy of combined therapies in MSS-CRC. Both propionic acid and B. fragilis improved CD8[+] T cell infiltration and treatment outcomes, with molecular assays indicating that propionic acid facilitates H3K14 acetylation, activating the Meox1-Cxcr6/Ccl5 axis.

CONCLUSIONS: This study highlights the pivotal role of the gut microbiome, specifically propionic acid and B. fragilis, in modulating the efficacy of combined radiotherapy and immunotherapy in MSS-CRC.}, } @article {pmid40706488, year = {2025}, author = {Tong, Y and Wang, Y and Zhang, J and Guo, Y and Yuan, T and Chen, H and Zhang, H and Zhan, K and Zhao, L and Ma, Q and Huang, S}, title = {Comprehensive study on the impact of ginger extract on laying performance, egg quality, inflammatory responses, intestinal barrier function, and cecal microbiome and resistome in laying hens.}, journal = {Poultry science}, volume = {104}, number = {10}, pages = {105448}, pmid = {40706488}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Zingiber officinale/chemistry ; Animal Feed/analysis ; Dietary Supplements/analysis ; Diet/veterinary ; *Plant Extracts/administration & dosage/metabolism ; Random Allocation ; Ovum/physiology/drug effects ; Inflammation/veterinary ; Cecum/microbiology ; *Reproduction/drug effects ; Intestines/drug effects/physiology ; *Immunity, Innate/drug effects ; Eggs/analysis ; Intestinal Barrier Function ; }, abstract = {Experimental models have been extensively used to explore the effects of ginger extract (GE) on oxidative stress and immune response. However, the influence of GE dietary supplementation on gut microbial composition, function, and the resistome in laying hens remains not fully understood. This research investigated the impact of GE supplementation on laying performance, egg quality, metabolism, inflammation, and the gut microbiome and resistome in laying hens. Thirty healthy, 35-week-old Jingfen No.6 laying hens with consistent body weight and laying rate were randomly allocated to either the control group (Con; basal diet) or the ginger extract supplementation group (Con-G; basal diet with 5 g/kg GE), each with fifteen replicates (one hen per replicate). The pre-feeding period lasted one week, followed by an eight-week trial. The results revealed that average laying rate (P = 0.051) and egg mass (P < 0.05) significantly increased, while feed conversion efficiency improved (P < 0.05) in the GE-supplemented group during the study period. Additionally, egg quality, host metabolism, serum antioxidant levels, and histological assessments of the jejunum, ileum, and cecum tissues were positively affected by GE (P < 0.05). Notably, GE supplementation significantly decreased (P < 0.05) serum pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) and increased (P < 0.05) IgA, IgG, and IL-10 levels. LEfSe analysis revealed that the relative abundance of genera such as Ligilactobacillus salivarius, Limosilactobacillus vaginalis, Butyricimonas virosa, and Limosilactobacillus alvi were significantly increased (P < 0.05) in the Con-G group. Furthermore, ginger extract significantly enhanced (P < 0.05) the production of short-chain fatty acids(including acetate, propionate, butyrate, isovalerate, valerate, and lactate) in the cecum, modulated the expression profile of antibiotic resistance genes in the intestines of laying hens, and inhibited pathogen colonization. The study concludes that ginger extract supplementation in laying hen diets improves laying performance, egg quality, host metabolism, and immune responses, positively alters gut microbiota composition and functionality, and modulates the poultry resistome. Metagenomic analysis underscores the potential of GE as a safe and effective additive.}, } @article {pmid40701001, year = {2025}, author = {Shang, H and Gou, W and Liu, S and Yuan, W and Cao, Z and Guo, Y and Zhang, N}, title = {Integrated metagenomics and metabolomic to reveal the effects of dietary comfrey polysaccharides on the oxidative stability and fatty acid composition of egg yolks in laying hens.}, journal = {Poultry science}, volume = {104}, number = {10}, pages = {105553}, pmid = {40701001}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/metabolism ; Diet/veterinary ; Female ; Animal Feed/analysis ; *Fatty Acids/metabolism/chemistry ; *Egg Yolk/chemistry/drug effects ; *Polysaccharides/metabolism/administration & dosage ; Metagenomics ; Oxidation-Reduction ; Metabolomics ; Dietary Supplements/analysis ; Gastrointestinal Microbiome/drug effects ; Random Allocation ; Antioxidants/metabolism ; }, abstract = {This study investigated the influences of comfrey (Symphytum officinale L.) polysaccharides (CPs) in the diet of laying hens on the oxidation stability and fatty acid composition of the egg yolks based on metagenomic and metabolomics techniques. Dietary CPs improved the total phenolic content in fresh and stored eggs. The activity of superoxide dismutase was increased, and the content of malondialdehyde was reduced in the stored eggs of the 1.0 % group of CPs. Dietary supplementation with 1.0 % CPs increased some polyunsaturated fatty acid (PUFA) contents in stored egg yolk, including dihomo-γ-linolenic acid (C20:3n6), arachidonic acid (C20:4n6), and docosahexaenoic acid (C22:6n3). The abundances of Methanobrevibacter, Parabacteroides, and Merdibacter in the caecum were increased in the 1.0 % group of CPs. The content of melatonin was increased, and the contents of palmitic acid and myristic acid in the caecum were decreased by CPs. These results suggested that CPs could improve the antioxidant status and fatty acid composition of egg yolks.}, } @article {pmid40663882, year = {2025}, author = {Khattak, F and Galgano, S and Pearson, R and Houdijk, JGM and Short, F and Leigh, A}, title = {Enhancing key broiler welfare indicators, meat quality, and gut microbiome composition using oxygen-enriched drinking water under commercially relevant housing conditions.}, journal = {Poultry science}, volume = {104}, number = {10}, pages = {105550}, pmid = {40663882}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/microbiology/growth & development ; *Meat/analysis ; *Animal Welfare ; Male ; *Drinking Water/chemistry/analysis ; *Oxygen/administration & dosage/analysis ; *Gastrointestinal Microbiome/drug effects ; Housing, Animal ; Random Allocation ; *Animal Husbandry/methods ; }, abstract = {Water is a critical nutrient in poultry production, yet its quality, particularly dissolved oxygen (DO) content, is often overlooked. This study is the first to comprehensively evaluate the impact of oxygen-enriched drinking water on broiler welfare, breast muscle myopathies, and gut microbiome composition under commercially relevant housing conditions. A total of 840 male Ross 308 broiler chicks were randomly assigned to two treatment groups (oxygenated water vs. tap water), with 12 replicate pens per treatment. Oxygenated water was enriched to a DO level of approximately 32 mg/L, compared to around 9.5 mg/L in tap water. Birds were reared to 36 days of age. The consistently high performance of both treatment groups under controlled experimental conditions is demonstrated by final body weights and feed conversion ratios surpassing Ross 308 breed standards by approximately 19-22 % from day 24 onward. Although growth performance remained unaffected under these optimal conditions, oxygenated water significantly improved welfare indicators, including feather condition, hock burn scores, and breast cleanliness (P< 0.05). Birds on oxygenated water also showed lower abdominal fat (-12 %) and higher thigh yield (+2.6 %) without compromising breast yield. Carcass fat deposition was significantly lower (abdominal fat pad reduced by ∼12 %), and thigh yield was higher in the oxygenated water treatment (P < 0.05), although overall carcass weight and breast yield were unchanged. No major differences were detected in breast meat nutrient composition (P > 0.05). The prevalence of white striping in breast fillets was markedly reduced in birds receiving oxygenated water, 32 mg/L indicating enhanced muscle integrity (P < 0.05). Metagenomic analysis revealed that some bacterial lipid metabolism pathways where differentially abundant in oxygenated-water birds. Following up on previous knowledge suggesting the interplay between lipid metabolism and broiler welfare, these findings suggest that supplementing broiler drinking water with 32 mg/L DO levels may offer a practical, non-pharmaceutical strategy to mitigate breast muscle myopathies and improve overall animal welfare and meat quality.}, } @article {pmid40464915, year = {2025}, author = {Kim, R and Oh, S and Woo, KA and Shin, CM and Park, KU and Lee, JY}, title = {Blood microbiome signatures in the REM sleep behavior disorder-Lewy body disease continuum.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {132}, number = {8}, pages = {1143-1154}, pmid = {40464915}, issn = {1435-1463}, mesh = {Humans ; *REM Sleep Behavior Disorder/microbiology/blood ; Male ; Female ; Aged ; Middle Aged ; *Lewy Body Disease/microbiology/blood ; *Microbiota/physiology ; *Parkinson Disease/microbiology/blood ; Biomarkers/blood ; Aged, 80 and over ; }, abstract = {Although systemic inflammation triggered by alterations in microbiota from various body sites has been proposed as a potential mechanism underlying Lewy body diseases (LBDs), the association between the blood microbiome and LBDs remains uncertain. This study aimed to investigate the blood microbiome profiles across the REM sleep behavior disorder (RBD)-LBD continuum and to explore their potential as biomarkers reflecting disease phenotypes and clinical severity. Blood samples were collected from 106 patients across the RBD-LBD continuum, including 41 with isolated RBD (iRBD), 45 Parkinson's disease with probable RBD, and 20 dementia with Lewy bodies with probable RBD, as well as from 94 healthy controls. All patients were evaluated with the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and comprehensive neuropsychological tests. Microbiome taxonomic compositions were analyzed using 16 S rRNA metagenomic sequencing. Significant microbial shifts were observed in the RBD-LBD continuum group compared to controls, with reduced microbial alpha diversity and distinct beta diversity patterns. Specifically, the genus Stenotrophomonas was enriched, while the genera Acetobacter, Enhydrobacter, and Lactobacillus were depleted in the RBD-LBD continuum group. The combined model using these genera demonstrated high predictive accuracy for the RBD-LBD continuum, with the area under the receiver-operating-characteristic curve (AUC) of 0.970 (95% confidence interval [CI]: 0.950-0.980). This model also successfully distinguished the iRBD subgroup from controls, achieving an AUC of 0.956 (95% CI, 0.914-0.987). Alpha and beta diversity were significantly associated with MDS-UPDRS Parts I and II scores in the RBD-LBD continuum group. Our findings suggest that patients within the RBD-LBD continuum may share specific blood microbiome signatures.}, } @article {pmid40037519, year = {2025}, author = {Jawale, N and Shenberger, JS and Rodriguez, RJ and Shetty, AK and Garg, PM}, title = {The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis.}, journal = {American journal of perinatology}, volume = {42}, number = {14}, pages = {1836-1845}, pmid = {40037519}, issn = {1098-8785}, support = {U54 GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428//NIGMS of the NIH/ ; }, mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/virology ; Infant, Newborn ; *Gastrointestinal Microbiome ; Infant, Premature ; Dysbiosis/microbiology ; Bacteriophages ; *Infant, Premature, Diseases/microbiology ; Mycobiome ; Virome ; Virus Diseases/complications ; }, abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..}, } @article {pmid41017911, year = {2025}, author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J}, title = {Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1649384}, pmid = {41017911}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Premature ; India/epidemiology ; Infant, Newborn ; *Enterocolitis, Necrotizing/microbiology/epidemiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Enterobacteriaceae/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is an inflammatory bowel disease that primarily affects preterm infants. Predisposing risk factors for NEC include prematurity, formula feeding, anemia, and sepsis. To date, no studies have investigated the gut microbiota of preterm infants with NEC in India.

METHOD: In the current study, shotgun metagenomic sequencing was performed on fecal samples from premature infants with NEC and healthy preterm infants (n = 24). Sequencing was conducted using the NovaSeq X Plus platform, generating 2 × 150 bp paired-end reads. The infants were matched based on gestational age and postnatal age.

RESULT: The median time to NEC diagnosis was 9 days (range: 1-30 days). Taxonomic analysis revealed a high prevalence of Enterobacteriaceae at the family level, with the genera Klebsiella and Escherichia particularly prominent in neonates with NEC. No statistically significant differences in alpha or beta diversity were observed between stool samples from infants with and without NEC. Linear regression analysis demonstrated that Enterobacteriaceae were significantly more abundant in stool samples from infants with NEC than without NEC (q < 0.05). Differential abundance analysis using Linear Discriminant Analysis Effect Size (LEfSe) identified Klebsiella pneumoniae and Escherichia coli as enriched in the gut microbiota of preterm infants with NEC. Functional analysis revealed an increase in genes associated with lipopolysaccharide (LPS) O-antigen, the type IV secretion system (T4SS), the L-rhamnose pathway, quorum sensing, and iron transporters, including ABC transporters, in stool samples from infants with NEC.

CONCLUSION: The high prevalence of Enterobacteriaceae and enrichment of LPS O-antigen and T4SS genes may be associated with NEC in Indian preterm infants.}, } @article {pmid41017909, year = {2025}, author = {Maan, S and Batra, K and Rajendhran, J and Joseph, R and Singh, VK and Chaudhary, D and Sindhu, S and Kadian, V and Kumar, A and Maan, NS and Mor, S}, title = {Exploring viral diversity in diarrheic porcine feces: a metagenomic analysis from an Indian swine farm.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1653342}, pmid = {41017909}, issn = {2235-2988}, mesh = {Animals ; Swine ; *Feces/virology ; *Swine Diseases/virology/epidemiology ; *Metagenomics ; India/epidemiology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Diarrhea/veterinary/virology ; Farms ; Genome, Viral ; Virome ; *Virus Diseases/veterinary/virology ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Pig husbandry is a vital sector in India, providing nutritional security and employment for marginalized communities. Pigs are advantageous due to high reproduction rates and fecundity, shorter generation intervals, and efficient feed conversion, requiring minimal housing. However, the swine industry encounters significant disease challenges, particularly viral gastroenteritis, which poses serious public health risks, especially in developing countries. Pigs serve as natural reservoirs and amplifiers for numerous viruses with zoonotic potential, making disease surveillance essential.

MATERIALS: In this study, we conducted a metagenomic analysis of 15 fecal samples from diarrheic pigs on a farm in India, marking the first exploration of the fecal virome diversity in this region. Our next-generation sequencing approach has enabled the unbiased detection of multiple viral agents in the porcine fecal samples, detecting both known and novel viral agents without prior target knowledge.

RESULTS: The key and novel viruses obtained in our study were porcine circovirus, porcine parvovirus 7, porcine mamastrovirus 3, porcine sapelovirus A, and porcine enterovirus G. This work resulted in the generation of full genomes for multiple porcine viruses, including Circovirus, Enterovirus, Sapelovirus, and Mamastrovirus, along with partial genomes of Parvovirus, Picobirnavirus, Porcine stool-associated RNA virus (Porcine Posavirus), Kobuvirus, and Rotavirus, all subjected to phylogenetic analysis.

CONCLUSION: Our survey indicates frequent co-infections with diverse viruses, creating conducive environments for viral recombination and reassortment. Continuous surveillance of viral pathogens in animal populations is essential for understanding the dynamics of both known and novel viruses and for detecting emerging pathogens, along with their zoonotic and pathogenic potential.}, } @article {pmid41015602, year = {2025}, author = {Nazrin, MRR and Pavan, JS and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Kamil, D and Subramanian, S}, title = {Host-Driven Functional Divergence in Gut Microbiota of Honeybees Apis cerana and Apis mellifera: Implications for Pollination, Nutrition, and Sustainable Apiculture.}, journal = {Current microbiology}, volume = {82}, number = {11}, pages = {531}, pmid = {41015602}, issn = {1432-0991}, mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Pollination ; }, abstract = {Honeybees are indispensable in sustaining natural ecosystems and global crop production by pollinating key food crops. Understanding their gut microbiota is crucial for insights into their health, nutrition, and behavior, with broader ecological and agricultural relevance. This study compares the gut microbiota of Apis cerana and Apis mellifera, focusing on bacterial composition, diversity, and functional roles. Using culture-dependent and metagenomic methods, core bacteria such as Lactobacillus, Fructobacillus, Gilliamella apicola, Bartonella apis, and Snodgrassella alvi were identified, linked to carbohydrate and nitrogen metabolism, immune modulation, and polysaccharide degradation. A. mellifera exhibited greater microbial and functional diversity, reflected in higher Shannon (1.22 vs. 1.08) and Simpson (0.675 vs. 0.655) indices. Strong intraspecies correlations and weaker interspecies correlations (Pearson's r = 0.6486) indicated distinct microbial profiles, supported by PCA (75.3% variation) and Adonis test (P = 0.04, R[2] = 0.723). Functional analysis via MG-RAST and UniFrac-based PCoA showed species-specific differences in key metabolic pathways. Enzymatic profiling revealed Fructobacillus fructosus with high invertase activity (7.31 ± 0.30) and Apilactobacillus apinorum with strong pectinolytic activity (4.707 ± 0.36), enhancing honeybee nutrition. These findings have significant implications for pollination efficiency, probiotic development, and sustainable apiculture, ultimately supporting conservation strategies and the resilience of honeybee populations.}, } @article {pmid40916941, year = {2025}, author = {Blecksmith, SE and Kalanetra, KM and Weng, CY and Suarez, C and Sitepu, IR and Tang, Y and Ehlers Cheang, S and Jiang, S and Cernioglo, K and Damian-Medina, K and Smilowitz, JT and Lebrilla, CB and Mills, DA and Lemay, DG}, title = {Fecal microbiomes from healthy adult consumers of fruits and vegetables exhibit fiber- and donor-specific fermentation: "5 a day" is not enough.}, journal = {Food & function}, volume = {16}, number = {19}, pages = {7561-7577}, pmid = {40916941}, issn = {2042-650X}, mesh = {Humans ; *Fruit/metabolism/microbiology ; *Feces/microbiology ; *Vegetables/metabolism/microbiology ; Fermentation ; Adult ; Male ; Female ; *Dietary Fiber/metabolism/analysis ; *Gastrointestinal Microbiome ; Middle Aged ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Young Adult ; Fatty Acids, Volatile/metabolism ; }, abstract = {To determine the fermentation capacity of gut microbiomes with diverse plant carbohydrate active enzyme (CAZyme) repertoires, we collected fecal samples from 18 healthy adults who reported consuming at least 5 different fruits and vegetables daily and conducted shotgun metagenome analysis. Five fecal samples with the most diverse CAZymes were then fermented in vitro with 7 different fibers selected for their unique monosaccharide profiles-banana, kale,13-bean soup, flax, coconut flour, MS Prebiotic (resistant starch) and Sunfiber (guar gum)-for 72 hours. Samples were collected at 4 timepoints for 16S sequencing, and pH, SCFAs, and monosaccharide measurements. The largest changes in pH, microbial diversity, monosaccharides, and short chain fatty acids (SCFAs) occurred in the first 24 hours of fermentation. SCFA production was highest with flax and lowest with coconut flour. Fermentation patterns ranged from little change to primary degradation (liberated monosaccharides) to robust production of SCFAs. Abundance of Bifidobacteriaceae, Butyricicoccaceae, and Ruminococcaceae correlated with the highest fermentation, Clostridiaceae, Enterococcaceae, and Eggerthellaceae with the lowest. Samples from three of the participants were more responsive than the other two. The donor-specific and fiber-specific responses seen in our study indicate that dietary guidance to consume 5 servings of fruits and vegetables per day may not be enough to ensure that our gut microbiota is capable of unlocking all of fiber's benefits.}, } @article {pmid41013611, year = {2025}, author = {Kazarina, A and Sarkar, S and Adams, B and Vogt, B and Rodela, L and Pogranichny, S and Powell, S and Wiechman, H and Heeren, L and Reese, N and Thompson, D and Ran, Q and Hartung, E and Akhunova, A and Akhunov, E and Johnson, L and Jumpponen, A and Lee, STM}, title = {Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {310}, pmid = {41013611}, issn = {1474-760X}, support = {2020-67019-3180//National Institute of Food and Agriculture/ ; 2238633//National Science Foundation CAREER Award/ ; OIA-1656006//National Science Foundation Award/ ; INV-004430/GATES/Gates Foundation/United States ; }, mesh = {*Rhizosphere ; *Stress, Physiological ; *Plant Roots/microbiology/metabolism ; *Droughts ; Soil Microbiology ; *Microbiota ; }, abstract = {BACKGROUND: Plants have evolved alongside microbes, enabling plants to better cope with abiotic and biotic stress. Interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants exhibit a "home field advantage" by preferentially recruiting microbes unique to their native environments, likely through mutual recognition and selective recruitment mechanisms.

RESULTS: Using gene- and genome-centric approaches, we assess the functional potential of root-associated microbes and profile their host metabolites to uncover the metabolic outputs potentially regulating host‒microbe interactions in Andropogon gerardii. We find that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine is highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses.

CONCLUSIONS: This study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance their ability to thrive in stressful environments. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture when coping with climate change.}, } @article {pmid41013568, year = {2025}, author = {Lei, Y and Zheng, Y and Yan, Y and Zhang, K and Sun, X and Yang, B and Ge, L and Meng, Z and Cao, X and Zhang, X and Yan, X and Xu, Y and Zhang, T and Shi, J and Chen, S and Qiu, Q and Chen, Y and Deng, L and Li, Z and Wang, X and Zhang, K}, title = {Deciphering functional landscapes of rumen microbiota unveils the role of Prevotella bryantii in milk fat synthesis in goats.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {311}, pmid = {41013568}, issn = {1474-760X}, support = {2022YFD1300203//the National Key Research and Development Program of China/ ; 2022ZD04014//the Biological Breeding-Major Projects/ ; CARS-39-03//the China Agricultural Research System/ ; 32402785//the National Natural Science Foundation of China/ ; 2024PT-ZCK-71-3//the Key Research and Development Program of Shaanxi Province/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Milk/metabolism ; *Prevotella/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Lactation ; *Microbiota ; Lipid Metabolism ; Niacinamide/metabolism ; }, abstract = {BACKGROUND: The rumen microbiome is critical for regulating milk synthesis in dairy livestock, yet the molecular mechanisms linking microbial functions to host lipid metabolism remain poorly understood. While host genetics and microbial composition have been studied, integrative analyses of the rumen-blood-mammary gland axis remain lacking.

RESULTS: Here, we present the goat rumen microbial reference gene catalog and 5514 metagenome-assembled genomes (MAGs) from 160 multi-breed rumen samples. Integrating this resource with lactation data from 177 Saanen dairy goats, we identify Prevotella spp. as keystone taxa driving concurrent increases in milk yield and fat percentage. Functional and metabolomic profiling reveals that Prevotella bryantii B14 synthesizes nicotinate, which is converted to nicotinamide in circulation. Using in vitro and in vivo models, we demonstrate that nicotinamide activates the mTORC1 pathway in mammary epithelial cells via GPR109A, which upregulates transcription factors SREBP and PPAR-γ and the downstream lipogenic genes FASN, ACCα, and SCD1 to promote milk fat synthesis. In contrast, the relative deficiency of P. bryantii B14 and the associated reduction in nicotinamide levels in the rumen of poor lactating dairy goats may represent a significant contributor to impaired lactation performance. Additionally, the enhanced hydrogenotrophic methanogenesis activity may also adversely affect their lactation phenotype.

CONCLUSIONS: Our study establishes a causal link between rumen microbial metabolism and mammary lipid synthesis mediated by nicotinamide-mTORC1 signaling and identifies Prevotella abundance as a biomarker for precision breeding. These findings advance the understanding of microbiome-host crosstalk in lactation and provide actionable strategies for enhancing dairy productivity through microbiota-targeted interventions.}, } @article {pmid41012703, year = {2025}, author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP}, title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091275}, pmid = {41012703}, issn = {1999-4915}, support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; }, abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.

METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.

RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.

CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.}, } @article {pmid41012679, year = {2025}, author = {Hernández, LHA and da Silva, FS and da Paz, TYB and Dias, DD and de Barros, BCV and Nunes, BTD and Casseb, LMN and da Silva, SP and da Costa Vasconcelos, PF and Cruz, ACR}, title = {Virome Analysis of Small Mammals from the Brazilian Amazon.}, journal = {Viruses}, volume = {17}, number = {9}, pages = {}, doi = {10.3390/v17091251}, pmid = {41012679}, issn = {1999-4915}, support = {3286/2013//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 88887.636166/2021-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 310295/2021-1//National Council for Scientific and Technological Development/ ; 406490/2023-6//National Council for Scientific and Technological Development/ ; 314522/2021-2//National Council for Scientific and Technological Development/ ; 406360/2022-7//Instituto Nacional de Ciência e Tecnologia em Viroses Emergentes e Reemergentes/ ; }, mesh = {Animals ; Brazil ; *Virome ; *Chiroptera/virology ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Opossums/virology ; *Rodentia/virology ; Animals, Wild/virology ; *Mammals/virology ; }, abstract = {The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health.}, } @article {pmid41011853, year = {2025}, author = {Saylam, E and Özden, Ö and Yerlikaya, FH and Sivrikaya, A and Yormaz, S and Arslan, U and Topkafa, M and Maçin, S}, title = {Investigation of Intestinal Microbiota and Short-Chain Fatty Acids in Colorectal Cancer and Detection of Biomarkers.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/pathogens14090953}, pmid = {41011853}, issn = {2076-0817}, support = {22401140//Selçuk University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/diagnosis/pathology/metabolism ; Male ; Female ; *Fatty Acids, Volatile/metabolism/analysis ; Middle Aged ; Feces/microbiology/chemistry ; Haptoglobins ; Aged ; Protein Precursors ; Acute-Phase Proteins/analysis ; Cholera Toxin/blood ; *Biomarkers, Tumor ; Carrier Proteins/blood ; Membrane Glycoproteins/blood ; Biomarkers ; Bacteria/classification/genetics/isolation & purification ; Adult ; }, abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide and a significant global health issue. The human gut microbiota, a complex ecosystem hosting numerous microorganisms such as bacteria, viruses, fungi, and protozoa, plays a crucial role. Increasing evidence indicates that gut microbiota is involved in CRC pathogenesis. In this study, the gut microbiota profiles, short-chain fatty acids, zonulin, and lipopolysaccharide-binding protein levels of newly diagnosed CRC patients were analyzed along with healthy controls to elucidate the relationship between CRC and the gut microbiota. The study included 16 newly diagnosed CRC patients and 16 healthy individuals. For microbiota analysis, DNA isolation from stool samples was performed using the Quick-DNA™ Fecal/Soil Microbe Miniprep Kit followed by sequencing using the MinION device. Data processing was conducted using Guppy software (version 6.5.7) and the Python (3.12) programming language. ELISA kits from Elabscience were utilized for analyzing LBP and zonulin serum levels. Fecal short-chain fatty acids were analyzed using GC-MS/MS equipped with a flame ionization detector and DB-FFAP column. Microbial alpha diversity, assessed using Shannon and Simpson indices, was found to be lower in CRC patients compared to healthy controls (p = 0.045, 0.017). Significant differences in microbial beta diversity were observed between the two groups (p = 0.004). At the phylum level, Bacteroidota was found to be decreased in CRC patients (p = 0.027). Potential biomarker candidates identified included Enterococcus faecium, Ruminococcus bicirculans, Enterococcus gilvus, Enterococcus casseliflavus, Segatella oris, and Akkermansia muciniphila. Serum zonulin levels were higher in CRC patients (CRC = 70.1 ± 26.14, Control = 53.93 ± 17.33, p = 0.048). There is a significant relationship between gut microbiota and CRC. A multifactorial evaluation of this relationship could shed light on potential biomarker identification and the development of new treatment options for CRC.}, } @article {pmid41011835, year = {2025}, author = {Ezzat, A and Abd El Wahed, A and Ceruti, A and El Asely, AM and Khalifa, MS and Winters, AD and Truyen, U and Shaheen, AA and Faisal, M}, title = {Exploring the Virome of Nile Tilapia (Oreochromis niloticus) Using Metagenomic Analysis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/pathogens14090935}, pmid = {41011835}, issn = {2076-0817}, mesh = {Animals ; *Cichlids/virology ; *Virome/genetics ; *Metagenomics/methods ; Phylogeny ; *Fish Diseases/virology ; *Viruses/genetics/classification/isolation & purification ; Egypt ; DNA Viruses/genetics/classification/isolation & purification ; Metagenome ; }, abstract = {Nile tilapia (Oreochromis niloticus) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is scarce information on the biology and epidemiology of these viruses. This exploratory metagenomic study used Oxford Nanopore Technology (ONT) sequencing to profile the virome compositions of both wild and farmed Nile tilapia across five regions in Egypt. The Nile tilapia virome was dominated by two double-stranded DNA bacteriophages, Muvirus mu and M. sfmu, which constituted 79.8% of the detected sequences. Eukaryotic viruses, including members of the families Amnoonviridae, Peribunyaviridae, and Baculoviridae, were also identified. Two giant DNA viruses known to infect Acanthamoeba spp., Mollivirus sp., and Pandoravirus sp. were identified in the spleen virome of tilapia from a single sampling site. The diversity analysis showed no significant differences among tissue types or sampling sites. Phylogenetic analyses were performed on a single virus detected of potential pathogenicity, an amnoonvirus. The analyses demonstrated that the detected virus is a member of the family Amnoonviridae and placed it alongside members of the Tilapinevirus genus. The virus, however, was distinct from the other two members in the genus: T. tilapae and T. poikilos. This study underscores the usefulness of ONT in providing a foundational understanding of the Nile tilapia virome.}, } @article {pmid41010985, year = {2025}, author = {Petrelli, F and Ghidini, A and Dottorini, L and Ghidini, M and Zaniboni, A and Tomasello, G}, title = {Clinical Evidence for Microbiome-Based Strategies in Cancer Immunotherapy: A State-of-the-Art Review.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {9}, pages = {}, doi = {10.3390/medicina61091595}, pmid = {41010985}, issn = {1648-9144}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immunotherapy/methods ; *Neoplasms/therapy ; Immune Checkpoint Inhibitors/therapeutic use ; Probiotics/therapeutic use ; }, abstract = {The gut microbiome has emerged as a critical determinant of immune-checkpoint inhibitor (ICI) efficacy. A narrative review of 95 clinical studies (2015-2025) shows that patients with greater gut microbial diversity and relative enrichment of commensals such as Akkermansia, Ruminococcus, and other short-chain fatty acid producers experience longer progression-free and overall survival, particularly in melanoma and non-small-cell lung cancer. Broad-spectrum antibiotics given within 30 days of ICI initiation and over-the-counter mixed probiotics consistently correlate with poorer outcomes. Early phase I/II trials of responder-derived fecal microbiota transplantation in ICI-refractory melanoma achieved objective response rates of 20-40%, while pilot high-fiber or plant-forward dietary interventions improved immunologic surrogates such as CD8[+] tumor infiltration. Machine-learning classifiers that integrate 16S or metagenomic profiles predict ICI response with an area under the ROC curve of 0.83-0.92. Methodological heterogeneity across sampling, sequencing, and clinical endpoints remains a barrier, underscoring the need for standardization and larger, well-powered trials.}, } @article {pmid41010544, year = {2025}, author = {Liu, Y and Kuang, W and Li, M and Wang, Z and Liu, Y and Zhao, M and Huan, H and Yang, Y}, title = {Cholesterol-Lowering Mechanism of Lactobacillus Bile Salt Hydrolase Through Regulation of Bifidobacterium pseudolongum in the Gut Microbiota.}, journal = {Nutrients}, volume = {17}, number = {18}, pages = {}, doi = {10.3390/nu17183019}, pmid = {41010544}, issn = {2072-6643}, support = {2024YFF0619500; no. BK20231280; CX(22)2019//National Key Research and Development Program of China; Natural Science Foundation of Jiangsu; Jiangsu Agriculture Science and Technology Innovation Fund/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Amidohydrolases/metabolism/pharmacology ; *Cholesterol/blood ; Mice ; Male ; *Bifidobacterium/growth & development/drug effects/metabolism ; *Lactobacillus/enzymology ; *Hypercholesterolemia/blood/microbiology ; Cholesterol 7-alpha-Hydroxylase/metabolism ; Fibroblast Growth Factors/metabolism ; Mice, Inbred C57BL ; *Anticholesteremic Agents/pharmacology ; Bile Acids and Salts/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Probiotics ; }, abstract = {Background: Cardiovascular diseases (CVDs) represent a major global health burden, and cholesterol reduction is a key strategy for their prevention and management. This study investigated the mechanism by which bile salt hydrolase (BSH) from Lactobacilli reduces cholesterol levels by modulating the growth of Bifidobacterium pseudolongum. Methods: The BSH-recombinant strain YB334 was administered to high-cholesterol-diet mice, and the cholesterol-lowering function of the strain was evaluated by assessing serum cholesterol parameters, including total cholesterol (TC), low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Metagenomic sequencing was used to analyze the gut microbiota, leading to the screening and acquisition of the "responsive" strains affected by BSH. Subsequent investigations were conducted into their cholesterol-lowering effects and mechanisms of action. Results: Oral administration of the BSH-recombinant strain YB334 can effectively reduce serum cholesterol levels in hypercholesterolemic mice while simultaneously leading to a significant increase in the abundance of B. pseudolongum within the gut microbiota. In vitro experiments indicated that this increased abundance might be closely associated with the strain's high tolerance to CA, the catalytic product of the BSH enzyme. The BPL-4 strain, obtained through screening, demonstrated cholesterol-lowering efficacy. Mechanistically, BPL-4 altered bile acid pool composition and modulated the farnesoid X receptor (FXR) signaling axis: it suppressed ileal FXR-fibroblast growth factor 15 (FGF15) expression, thereby de-repressing hepatic cholesterol 7α-hydroxylase (CYP7A1) and accelerating cholesterol catabolism into bile acids. Conclusions: This study provides the first evidence that BSH from lactobacilli can shape the signature gut microbiota by modulating bile acid metabolism via the FXR-CYP7A1 axis, thereby demonstrating a mechanism for its cholesterol-lowering effects.}, } @article {pmid41009770, year = {2025}, author = {Pita-Galeana, MA and Ruhle, M and López-Vázquez, L and de Anda-Jáuregui, G and Hernández-Lemus, E}, title = {Computational Metagenomics: State of the Art.}, journal = {International journal of molecular sciences}, volume = {26}, number = {18}, pages = {}, doi = {10.3390/ijms26189206}, pmid = {41009770}, issn = {1422-0067}, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Machine Learning ; Metagenome ; }, abstract = {Computational metagenomics has revolutionized our understanding of the human microbiome, enabling the characterization of microbial diversity, the prediction of functional capabilities, and the identification of associations with human health outcomes. This review provides a concise yet comprehensive overview of state-of-the-art computational approaches in metagenomics, alongside widely used methods and tools employed in amplicon-based metagenomics. It is intended as an introductory resource for new researchers, outlining key methodologies, challenges, and future directions in the field. We discuss recent advances in bioinformatics pipelines, machine learning (ML) models, and integrative frameworks that are transforming our understanding of the microbiome's role in health and disease. By addressing current limitations and proposing innovative solutions, this review aims to outline a roadmap for future research and clinical translation in computational metagenomics.}, } @article {pmid41007466, year = {2025}, author = {Godoy-Vitorino, F}, title = {Strengthening Integrative Microbiome Research Through Regional Leadership.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {9}, pages = {}, doi = {10.3390/ijerph22091322}, pmid = {41007466}, issn = {1660-4601}, support = {1P20GM156713-01/GM/NIGMS NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; 2U54MD007600//Center for Collaborative Research in Minority Health and Health Disparities/ ; }, mesh = {*Microbiota ; Puerto Rico ; Leadership ; Humans ; Metagenomics ; Research/organization & administration ; }, abstract = {Microbiome science has revolutionized modern biology, shifting the focus from pathogens to the essential roles of beneficial microbes in health, metabolism, and ecosystems. Advances in genomic technologies like metagenomics have rapidly expanded our understanding of microbial diversity and function. Despite this progress, global microbiome research remains concentrated in high-resource regions, limiting diverse perspectives and opportunities in places like the Caribbean. This communication discusses the establishment of the first Center for Microbiome Sciences in Puerto Rico, which addresses this gap by providing local researchers with access to advanced tools, training, and infrastructure through broader collaboration. Novelty, services, and ideas on the integration of activities among local centers for the scientific improvement of the region are addressed. Additionally, how the center is poised to contribute to improving public and environmental health is also highlighted.}, } @article {pmid41006795, year = {2025}, author = {Aoyagi, LN and Wang, Y and Ohbayashi, T and Hirono, Y and Hayatsu, M and Tago, K}, title = {Diversity and characterization of the ammonia-oxidizing bacteria responsible for nitrification in tea field soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33221}, pmid = {41006795}, issn = {2045-2322}, support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; 16K14874//MEXT KAKENHI/ ; 19H01156//MEXT KAKENHI/ ; 28004A//Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries, and Food Industry/ ; }, mesh = {*Nitrification ; *Ammonia/metabolism ; *Soil Microbiology ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil/chemistry ; Archaea/metabolism/genetics/classification ; Phylogeny ; *Tea/microbiology ; Biodiversity ; }, abstract = {Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and comammox Nitrospira have been considered to coexist in acidic soils, oxidizing ammonia within their respective niches. However, their relative contributions to soil nitrification, as well as their properties and ecological roles in acidic soils, remain poorly understood. This study focused on AOB in acidic tea field soils, investigating their ecology and physiology through metagenomic analysis and the genomic and physiological characterization of AOB isolates. β-AOB were significantly more abundant than γ-AOB and AOA in soil layers with the highest potential for nitrification activity, indicating that β-AOB play a key role in acidic tea soil. Diversity analysis of this dominant group identified Nitrosospira as the major genus present in tea fields, and four pure strains representing some of the main operational taxonomic units in this environment were isolated. Physiological and genetic characterization of these isolates revealed some distinct traits compared to other species of the genus and closely related taxa, suggesting adaptations that may contribute to niche differentiation and survival in acidic soils. These findings provide new insights into the ecological role of β-AOB in acidic soils and may inform strategies to manage soil nitrification and reduce nitrogen loss in agricultural ecosystems.}, } @article {pmid41006325, year = {2025}, author = {Zhang, L and Zhou, DD and Feng, J and Liao, ZJ and Shu, XL and Yang, RM and Gao, YC and Zhou, HH and Zhang, W and Zou, Y and Liu, R}, title = {Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {188}, pmid = {41006325}, issn = {2055-5008}, support = {2021YFA1301200//the National Key Research and Development Program/ ; No. 82474022, 31801121, 82373961//the National Scientific Foundation of China/ ; 2022RC1022//the Hunan Provincial Science and Technology Innovation Plan Project/ ; }, mesh = {*Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Fungi/classification/genetics/isolation & purification ; Animals ; Mice ; Feces/microbiology ; Cohort Studies ; *Neoplasms/drug therapy/microbiology ; }, abstract = {Gut microbiota influence on the effectiveness of immune checkpoint inhibitors (ICIs), but research on fungi-an essential component of the microbiome-has been limited. This multi-cohort meta-analysis of 976 fecal metagenomes across 8 cohorts, representing melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC), identified fungal species associated with ICI efficacy. In melanoma, Rhizophagus irregularis and Debaryomyces hansenii were correlated with poor responses, whereas Aspergillus avenaceus was associated with great efficacy. In NSCLC, an increased abundance of Aspergillus pseudonomiae was associated with a favorable prognosis. Stronger bacterial-fungal interactions were observed in responders. The presence of certain fungi in fungal enterotypes, like Aspergillus or Saccharomyces, was linked to better efficacy to ICIs. Mouse models revealed Debaryomyces hansenii impaired ICI efficacy by reducing CD8+ T cells. Our findings highlight specific fungal signatures that may inform strategies to enhance ICI efficacy and encourage further research on microbial impacts on treatment outcomes.}, } @article {pmid40344212, year = {2025}, author = {Zhao, Y and Song, L and Li, HY and Liu, SX and Mao, FF and Li, XJ and Ding, PH}, title = {Metagenomic Insights Into the Subgingival Microbiome in Periodontal Health and Different Grades of Periodontitis.}, journal = {Journal of periodontal research}, volume = {60}, number = {8}, pages = {788-798}, doi = {10.1111/jre.13408}, pmid = {40344212}, issn = {1600-0765}, support = {//Postdoctoral Science Foundation of China/ ; //National Natural Science Foundation of China/ ; //the Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; //National Key Research and Development Program of China/ ; //Key Research and Development Program of Zhejiang Province/ ; //Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; *Periodontitis/microbiology/classification ; *Microbiota/genetics ; Female ; Cross-Sectional Studies ; *Metagenomics ; Adult ; Middle Aged ; *Gingiva/microbiology ; Male ; Capnocytophaga/genetics ; }, abstract = {AIM: This cross-sectional study compared the subgingival microbiome in periodontal health (PH) and periodontitis, focusing on distinguishing Stage III Grade B periodontitis (PD-S3gB) and Stage III Grade C periodontitis (PD-S3gC) as defined by the 2018 Classification of Periodontitis.

METHODS: Subgingival samples from subjects with PH, PD-S3gB, and PD-S3gC were analyzed using metagenomic sequencing. Taxonomic and functional annotations were performed, followed by analyses of microbial diversity, differential abundance, interspecies networks, predictive modeling, and functional pathway enrichment.

RESULTS: Significant differences in both alpha and beta diversity were observed between PH and periodontitis. Several periodontal pathogens were more abundant in disease states, with Capnocytophaga granulosa and Capnocytophaga sp. CM59 enriched in PD-S3gC compared to PD-S3gB. The PD-S3gC group also exhibited a more complex microbial network with increased interspecies connectivity. An 11-species diagnostic model effectively distinguished PH, PD-S3gB, and PD-S3gC. Furthermore, pathways related to motility, chemotaxis, and methane metabolism were significantly enriched in periodontitis.

CONCLUSION: Distinct structural and functional differences in the subgingival microbiome characterize periodontal health and periodontitis. Periodontitis with a rapid rate of progression is marked by specific pathogen overgrowth and enhanced microbial interactions, supporting the development of microbiome-based diagnostics and personalized therapies.

TRIAL REGISTRATION: Chinese Clinical Trial Registration: ChiCTR2000039426.}, } @article {pmid41005935, year = {2026}, author = {Yang, W and Xin, X and Cao, X}, title = {Impacts of trace ofloxacin on autotrophic denitrification process driven by pyrite/sulfur: Performance, microbial community evolution and metagenomic analysis.}, journal = {Journal of environmental sciences (China)}, volume = {159}, number = {}, pages = {775-784}, doi = {10.1016/j.jes.2025.03.062}, pmid = {41005935}, issn = {1001-0742}, mesh = {*Denitrification/drug effects ; Autotrophic Processes ; *Water Pollutants, Chemical/toxicity/analysis ; Sulfides/chemistry ; *Ofloxacin/toxicity/analysis ; Sulfur/chemistry ; Iron/chemistry ; Metagenomics ; *Microbiota/drug effects ; Anti-Bacterial Agents/toxicity ; Bioreactors ; }, abstract = {In this work, ofloxacin (OFL), a kind of frequently detected antibiotic in groundwater, was selected to explore its impact (at ng/L-µg/L-level) on denitrification performance in an autotrophic denitrification system driven by pyrite/sulfur (FeS2/S[0]). Results showed that OFL restrained nitrate removal efficiency, and the inhibition degree was positively related to the concentration of OFL. After being exposed to increased OFL (200 ng/L-100 µg/L) for 69 days, higher inhibition of electron transport activity (ETSA), enzyme activities of nitrate reductase (NAR), and nitrite reductase (NIR) were acquired. Meanwhile, the extracellular protein (PN) content of sludge samples was remarkably stimulated by OFL to resist the augmented toxicity. OFL contributed to increased microbial diversity and sulfur/sulfide oxidation functional genes in ng/L-level bioreactors, whereas led to a decline in µg/L level experiments. With OFL at concentrations of 200 ng/L and 100 µg/L, the whole expression of 10 key denitrification functional genes was depressed, and the higher the OFL concentration, the lower the expression level. However, no significant proliferation of antibiotic resistance genes (ARGs) either in 200 ng/L-OFL or 100 µg/L-OFL groups was observed. Two-factor correlation analysis results indicated that Thiobacillus, Anaerolineae, Anaerolineales, and Nitrospirae might be the main hosts of existing ARGs in this system.}, } @article {pmid41005808, year = {2025}, author = {Purcell, M and Ackland, J and Staples, KJ and Freeman, A and Wilkinson, TMA}, title = {The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {34}, number = {177}, pages = {}, doi = {10.1183/16000617.0284-2024}, pmid = {41005808}, issn = {1600-0617}, mesh = {Humans ; *Virome ; *Viruses/genetics/pathogenicity/immunology ; Host-Pathogen Interactions ; *Microbiota ; *Respiratory System/virology ; *Respiratory Tract Infections/virology ; Metagenomics ; *Respiratory Tract Diseases/virology/diagnosis ; Animals ; }, abstract = {The human respiratory tract virome is an underexplored component of the microbiome that includes eukaryotic viruses, bacteriophages and archaeal viruses. The respiratory virome represents a dynamic and heterogeneous ecosystem, shaped by host, environmental and microbial factors. Advances in metagenomic sequencing have expanded our understanding of virome composition, dynamics and potential roles in health and disease. Despite increasing interest, virome research remains fragmented and often secondary to bacteriome studies. Challenges in study design, genomic characterisation and interpretation limit consistent conclusions. This review summarises current knowledge of the respiratory virome in health and across acute and chronic respiratory diseases, including acute respiratory infection, asthma, COPD, cystic fibrosis and bronchiectasis. While each condition is distinct, they share features of airway inflammation and immune dysregulation where the virome may act as a modifier or marker. Across these syndromes, emerging evidence highlights the consistent detection of respiratory viruses including potential commensals, such as Anelloviridae, and the often-overlooked role of bacteriophages. We also discuss the concept of viral dark matter, where large proportions of sequence data remain unclassified, potentially representing novel viral taxa. Technical and conceptual challenges are evaluated, alongside recent methodological innovations such as meta-transcriptomics and viral enrichment protocols. We outline how standardised, multi-omic and longitudinal approaches are urgently needed to clarify the virome's functional role, interactions with immunity and microbial communities and its utility as a biomarker or therapeutic target.}, } @article {pmid40999698, year = {2025}, author = {Elliott, L and Coissac, E}, title = {Can Amplicon Sequencing Be Replaced by Metagenomics for Biodiversity Inventories?.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70047}, doi = {10.1111/1755-0998.70047}, pmid = {40999698}, issn = {1755-0998}, support = {819192//European Research Council (ERC)/ ; }, } @article {pmid40998902, year = {2025}, author = {Satpathy, SS and Pradhan, D}, title = {Unveiling community structure, antimicrobial resistance, and virulence factor of a wastewater sample of dairy farm located in mayurbhanj, odisha, India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32919}, pmid = {40998902}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; India ; *Virulence Factors/genetics ; *Dairying ; *Bacteria/genetics/drug effects/pathogenicity/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Farms ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Water Microbiology ; }, abstract = {Nutrient-rich dairy wastewater (DWW) is an excellent growing medium for microbes. Their antimicrobial resistance (AMR) genes and pathogenic roles remain in the DWW and even multiply in environmental settings, in contrast to many chemical toxins that break down over time. Necessary steps and standardized techniques for tracking AMR in DWW samples are desperately needed. In this context, a DWW sample was evaluated to assess the necessity of remediation and develop a suitable treatment technique. Physicochemical characterizations of the sample showed an elevated level of pollutants like proteins, fats, and carbohydrates that led to the water pollution and microbial diversity (e.g., 36 phyla, 72 classes, 111 orders, 168 families, 275 genera, and 347 species). The Shannon and Simpson indices showed that the DWW sample had a high level of microbial diversity of a few species. The gene ontology (GO) analysis revealed the functional categories with 2795 genes belonging to 11 virulence categories. Most of the identified AMR genes belonged to beta-lactamase, and the majority of them were linked to Escherichia coli, Mycobacterium tuberculosis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, etc. The major bacterial phyla carrying AMR genes included Firmicutes (36%), Proteobacteria (31%), Actinobacteria (21%), and Bacteroidetes (5%).}, } @article {pmid40848105, year = {2025}, author = {Proskynitopoulos, PJ and Woltemate, S and Rhein, M and Böke, I and Molks, J and Schröder, S and Schneider, HU and Bleich, S and Frieling, H and Geffers, R and Glahn, A and Vital, M}, title = {The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.}, journal = {Alcohol, clinical & experimental research}, volume = {49}, number = {9}, pages = {1912-1923}, doi = {10.1111/acer.70128}, pmid = {40848105}, issn = {2993-7175}, support = {//Hetzler Foundation for Addiction Research and Prevention/ ; }, mesh = {Humans ; *Craving/physiology/drug effects ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Female ; Middle Aged ; *Alcoholism/microbiology/therapy ; Adult ; *Substance Withdrawal Syndrome/microbiology ; *Inflammation ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {BACKGROUND: Alcohol use disorder (AUD) is linked to changes in the function and composition of the human gut microbiome (GM). The GM affects inflammation by producing anti-inflammatory molecules such as short-chain fatty acids (SCFA), in particular butyrate, which are linked to appetite regulation, a mechanism involved in alcohol craving. This study investigates changes in GM composition and functional capacity to produce SCFA during alcohol withdrawal and their link to inflammation and craving.

METHODS: Sixty-three patients (mean age 48, SD = 12) with AUD were enrolled. We collected stool (n = 63) and blood (n = 48) during the first 48 h (timepoint A) of withdrawal therapy and between Days 10-14 (timepoint B). Microbiota were analyzed using shotgun metagenomics along with bacterial load determinations. TNF-α, IL-6, IL-8, and IL-10 were measured in plasma.

RESULTS: Bacterial diversity (species richness, Shannon Index) did not change significantly throughout withdrawal, while overall bacterial load increased. Abundances of several taxa changed, and the overall community composition during withdrawal was approaching those of healthy controls; the potential to synthesize butyrate, a key SCFA, increased. However, it remained at lower levels compared with controls. Both diversity parameters correlated with cell concentrations and the butyrate pathway at baseline. The latter was negatively associated with IL-6 at baseline. IL-8 and IL-10 levels decreased significantly during withdrawal, as did craving, which was linked to abundance alterations of six species and IL-8.

CONCLUSIONS: Alcohol withdrawal affected GM composition and increased concentration of the butyrate pathway along with overall bacterial load. Changes in bacterial composition and the butyrate production capacity demonstrate a shift toward healthier microbiota during withdrawal therapy. Changes in some species and IL-8 were linked to alcohol craving, replicating findings of previous studies. Our study adds new findings helping to understand the microbiome-gut-brain axis.}, } @article {pmid40833852, year = {2025}, author = {Vander Donck, L and Victor, M and Van Beeck, W and Van Rillaer, T and Dillen, J and Ahannach, S and Wittouck, S and Allonsius, CN and Lebeer, S}, title = {Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.}, journal = {Cell reports}, volume = {44}, number = {9}, pages = {116171}, pmid = {40833852}, issn = {2211-1247}, mesh = {Female ; Humans ; *Vagina/microbiology ; *Lactobacillus crispatus/physiology/genetics ; Microbiota ; *Lactobacillus/physiology/genetics ; }, abstract = {The human vagina is a unique microbiome, typically predominated by Lactobacillus species in healthy women. However, we currently lack an understanding of why lactobacilli predominate in this environment and how these bacteria interact, aspects that are crucial for developing microbiome-based therapeutics. In this study, we used cost-efficient synthetic communities (SynComs) to investigate the stability and dynamics of Lactobacillus-predominated vaginal communities from healthy women independent of host influence. Reproducible communities of Lactobacillus crispatus co-occurring with Limosilactobacillus species and Lactobacillus jensenii were established in top-down experiments. Co-occurrence was verified with compositional correlation patterns in metagenome sequencing data and reproduced through a bottom-up approach. This co-occurrence pattern was independent of strain selection, host factors, and inoculation ratio. Genome-scale metabolic models predicted potential cross-feeding involving amino acids (e.g., L-arginine, L-lysine, and γ-aminobutyric acid [GABA]) and vitamins as mechanisms mediating their co-occurrence. This study provides a framework for developing reproducible synthetic vaginal Lactobacillus communities and informs future microbiome-based therapies.}, } @article {pmid40996787, year = {2025}, author = {Bergner, L and Catalano, S and Nichols, J and Da Silva Felipe, A and Cao, X and Mair, D and Nankasi, A and Arinaitwe, M and Mubangizi, A and Pybus, OG and Standley, C and Faust, CL and Raghwani, J}, title = {Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing.}, journal = {Microbial genomics}, volume = {11}, number = {9}, pages = {}, doi = {10.1099/mgen.0.001513}, pmid = {40996787}, issn = {2057-5858}, mesh = {Animals ; *Viral Load ; *Metagenomics/methods ; Feces/virology ; *Animals, Wild/virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics/classification/isolation & purification ; RNA Viruses/genetics/isolation & purification ; DNA Viruses/genetics/isolation & purification ; Rodentia/virology ; }, abstract = {Metagenomics is a powerful tool for characterizing viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causative agents of emerging outbreaks with unknown aetiology. Additionally, metagenomic data contain valuable information about the amount of virus present within samples (i.e. viral load), which can provide insights into transmission potential, time since infection and, in turn, epidemic trajectories. However, before we can effectively use metagenomic data to inform transmission, we need to understand the general relationship between sequencing outputs and viral load. Here, using a commercially available probe panel targeting a wide diversity of viruses, we investigated the detection and recovery of virus genomes by spiking known concentrations of DNA and RNA viruses into wild rodent faecal samples. In total, 15 experimental replicates were sequenced with target enrichment sequencing and compared to shotgun sequencing of the same background samples. Target-enriched sequencing recovered all spike-in viruses at every concentration (10[2], 10[3] and 10[5]±1 log genome copies) and showed a log-linear relationship between spike-in concentration and mean read depth. Background viruses (including Kobuvirus and Cardiovirus) were recovered consistently across all biological and technical replicates and by shotgun sequencing, but genome coverage was variable between virus genera and likely reflected the composition of the target enrichment probe panel. Overall, our study highlights the strengths and weaknesses of using commercially available panels to quantify and characterize wildlife viromes and underscores the importance of probe panel design for accurately interpreting coverage and read depth. To advance the use of metagenomics for understanding virus transmission, further research will be needed to elucidate how sequencing strategy (e.g. library depth and pooling), virome composition and probe design influence viral read counts and genome coverage.}, } @article {pmid40996703, year = {2025}, author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE}, title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, doi = {10.1093/database/baaf060}, pmid = {40996703}, issn = {1758-0463}, support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; }, mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; }, abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.}, } @article {pmid40995781, year = {2025}, author = {Hensen, T and Thiele, I}, title = {Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2554195}, doi = {10.1080/19490976.2025.2554195}, pmid = {40995781}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/metabolism/blood ; Male ; Female ; Biomarkers/blood/metabolism ; Middle Aged ; Aged ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics ; Leucine/metabolism/blood ; }, abstract = {Human gut microbiota have been implicated in metabolic disruptions in Parkinson's disease (PD). However, the underlying mechanisms linking gut microbiota to these disease-related metabolic changes remain largely unknown. In this study, we applied constraint-based metabolic modeling to identify potential causal links between compositional shifts in gut microbiota in PD and metabolic blood markers of PD. We personalized in silico whole-body metabolic models with gut metagenomics of 435 PD patients and 219 healthy controls and profiled in silico gut microbiome influences on 116 blood metabolites with replicated associations with PD diagnosis. Our analysis identified a reduced capacity of the PD host-microbiome co-metabolism to produce L-leucine and leucylleucine in blood. These metabolic predictions were traced back to lower L-leucine production of Roseburia intestinalis and higher L-leucine consumption by Methanobrevibacter smithii in PD microbiomes. We further predicted reduced host-microbiome production capacities of butyrate, myristic acid, and pantothenate in the blood of PD patients and linked these associations to reduced relative abundances of Faecalibacterium prausnitzii. Finally, lower nicotinic acid production capacities were predicted in PD patients, which were associated with increased relative abundances and increased nicotinic acid consumption of Ruthenibacterium lactatiformans in PD. In conclusion, we predicted that the gut microbiome can drive altered blood levels of six metabolites in PD and identified candidate microbial species that may influence these metabolic alterations. These findings may facilitate the development of novel therapies targeting the gut-brain axis in PD.}, } @article {pmid40995227, year = {2025}, author = {Lee, SH and Kim, EB and Park, SC and Nam, SJ and Cho, H and Jeon, HJ and Lee, SP}, title = {Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1651316}, pmid = {40995227}, issn = {2235-2988}, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Body Mass Index ; Female ; Male ; Middle Aged ; Obesity/microbiology ; *Gastrointestinal Microbiome/genetics ; Adult ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; DNA, Ribosomal/chemistry/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Overweight/microbiology ; Metagenomics ; Phylogeny ; }, abstract = {INTRODUCTION: Obesity is a multifactorial condition influenced by various factors, including the gut microbiota. However, the relationship between the gastric microbiota and obesity remains poorly understood. This study aimed to investigate the composition of gastric microbiota, excluding Helicobacter pylori, in relation to body mass index (BMI) and metabolic indicators.

METHODS: Thirty participants undergoing health checkups were classified into three groups-normal weight (BMI 18.5-22.9), overweight (BMI 23.0-24.9), and obese (BMI ≥25.0)-with ten individuals per group. Those with H. pylori infection, atrophic gastritis, or intestinal metaplasia were excluded. Gastric microbiota from four antral biopsies per subject were analyzed using 16S rRNA sequencing and functional profiling by metagenomic prediction.

RESULTS AND DISCUSSION: Alpha diversity (Gini-Simpson index) was significantly lower in the combined overweight/obese group than that in the normal group (P=0.049). Beta diversity analysis revealed clear group separation (Bray-Curtis, P=0.005; unweighted UniFrac, P=0.004). Significant species differences between the groups were observed; specifically, the abundances of Muribaculum gordoncarteri, Turicibacter bilis, and Duncaniella dubosii, were significantly reduced in the overweight/obese group. Functional predictions showed differential enrichment of pathways related to fatty acid, amino acid, vitamin, and carbohydrate metabolism across BMI categories. These findings suggest that alterations in the gastric microbiota may be linked to obesity and metabolic dysregulation.}, } @article {pmid40993967, year = {2025}, author = {Bibbò, S and Ahlström, G and Pes, GM and Graham, DY and Engstrand, L and Merola, E and Dore, MP}, title = {Resilience of the Gut Microbiome to Short Proton Pump Inhibitor Therapy With or Without High-Dosage L. reuteri in H. pylori-Infected Adults.}, journal = {Helicobacter}, volume = {30}, number = {5}, pages = {e70064}, doi = {10.1111/hel.70064}, pmid = {40993967}, issn = {1523-5378}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Limosilactobacillus reuteri/physiology/growth & development ; *Helicobacter Infections/drug therapy/microbiology ; *Proton Pump Inhibitors/therapeutic use/administration & dosage ; Female ; Male ; Middle Aged ; Double-Blind Method ; Adult ; Pantoprazole/therapeutic use ; *Probiotics/administration & dosage ; Helicobacter pylori/drug effects ; Feces/microbiology ; Aged ; }, abstract = {BACKGROUND: Helicobacter pylori eradication therapy typically consists of a combination of antibiotics and an antisecretory drug. Probiotics may be added to reduce side effects and possibly improve outcomes.

MATERIALS AND METHODS: We conducted a double-blind, randomized trial of pantoprazole plus either Lactobacillus reuteri (Gastrus) (high dose) or a matching placebo to assess the impact on the gut microbiota of H. pylori-positive adults. Fecal samples were collected at baseline and after one and 2 months for shotgun metagenomic sequencing.

RESULTS: A total of 26 patients were recruited and completed therapy. L. reuteri was only detected in the group that received supplemental L. reuteri and only at the 1-month post-treatment interval. L. reuteri failed to colonize for long-term the gut, and challenge with L. reuteri failed to alter alpha-diversity (Shannon index) or beta-diversity (community ordination) metrics at any time point. Machine learning (PLS-DA) analysis identified the presence of L. reuteri as the most distinguishing feature at 1 month. No other taxa showed a significant difference between groups.

CONCLUSION: Short-term administration of pantoprazole and L. reuteri had no lasting effects on gut microbial composition. While L. reuteri transiently bloomed during supplementation, the overall gut microbiota showed resilience, returning to baseline shortly after therapy.

TRIAL REGISTRATION: Identifier: NCT03404440.}, } @article {pmid40993109, year = {2025}, author = {Zeng, Y and Zhong, X and Chai, L and Zhang, X and Lu, Z and Liu, G and Tu, T and Lu, L and Zhang, R and Yu, H and Zhang, S and Wang, S and Shen, C and Shi, J and Xu, Z}, title = {Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {186}, pmid = {40993109}, issn = {2055-5008}, support = {32201993//National Natural Science Foundation of China/ ; 31901658//National Natural Science Foundation of China/ ; 2024T170375//China Postdoctoral Science Foundation/ ; }, mesh = {*Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbial Consortia ; Ecosystem ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Fermentation ; Phylogeny ; }, abstract = {Elucidating the temporal dynamics of complex microbial consortia is crucial for engineering robust microbiome. We investigated prokaryotic evolution in pit mud, a centuries-old engineered environment used in Chinese liquor fermentation. Metagenomic analysis of 120 pit mud samples across different ages revealed a transition from generalist-dominated to specialist-enriched communities. This shift was characterized by decreased hydrolytic potential and increased organic acid metabolism, with key taxonomic changes including declines in Proteiniphilum and Petrimonas, and increases in Methanobacterium and Caproicibacter. The mature specialist community accelerates the short-chain organic acids turnover through syntrophic fatty acid oxidation, methanogenesis, and carbon chain elongation, maintaining ecosystem stability. While nutrient availability primarily shapes early stages community interactions, environmental stress becomes a dominant factor in mature systems. These insights into long-term prokaryotic adaptation provide a foundation for the rational design of resilient, functionally optimized microbial communities for biotechnological applications.}, } @article {pmid40880127, year = {2025}, author = {Milnitsky, BP and Junior, HLP and Chaúque, BJM and Corção, G}, title = {Successful establishment of a model of the piglet gastrointestinal microbiota and its' modulation by prebiotics.}, journal = {Journal of applied microbiology}, volume = {136}, number = {9}, pages = {}, doi = {10.1093/jambio/lxaf216}, pmid = {40880127}, issn = {1365-2672}, support = {//National Council for Scientific and Technological Development/ ; //Universidade Federal do Rio Grande do Sul/ ; }, mesh = {Animals ; *Prebiotics ; Swine/microbiology ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; *Bacteria/drug effects/classification/isolation & purification/genetics ; Microbial Sensitivity Tests ; Butyric Acid/pharmacology ; Anti-Bacterial Agents/pharmacology ; Oligosaccharides/pharmacology ; *Gastrointestinal Tract/microbiology ; }, abstract = {AIMS: This study proposed an in-house in vitro model to investigate the effects of two prebiotic treatments on the gastrointestinal microbiota of piglets.

METHODS AND RESULTS: The model involved suspending piglet feces in a culture medium to simulate the ileum and proximal colon regions of the swine gastrointestinal tract. The prebiotics tested were mannanoligosaccharides (MOS) and sodium butyrate. Metabarcoding and culturomics were used to assess the impact of prebiotics on bacterial species composition. Minimum inhibitory concentration tests were conducted to examine bacterial susceptibility patterns. Key bacterial phyla identified included firmicutes, proteobacteria, bacteroidetes, and actinobacteria. Culturomics detected families and several species not identified by metabarcoding. In the simulated proximal colon, MOS increased the abundance of certain species and reduced bacteria with type I fimbriae. Butyric acid promoted beneficial host-associated bacteria and decreased pathogenic species. However, the prebiotics did not significantly affect bacterial susceptibility to antibiotics.

CONCLUSION: The in-house model successfully mimicked piglet intestinal microbiota, allowing for detailed analysis. Both prebiotics positively influenced the piglets microbiota, providing insights into how these treatments potentially influenced the microbiota.}, } @article {pmid40602513, year = {2025}, author = {Zhang, Z and Wang, X and Yang, L and Cui, Y and Zhang, Z}, title = {Soil redox-adaptive anode potentials enhance microbial electroactivity through targeted enrichment of exoelectrogenic consortia in paddy soil.}, journal = {Environmental research}, volume = {284}, number = {}, pages = {122265}, doi = {10.1016/j.envres.2025.122265}, pmid = {40602513}, issn = {1096-0953}, mesh = {*Soil Microbiology ; Oxidation-Reduction ; Electrodes ; *Soil/chemistry ; Bacteria/metabolism ; *Microbial Consortia ; *Bioelectric Energy Sources ; Geobacter ; }, abstract = {Exoelectrogenic bacteria (EEB) act as critical drivers in terrestrial and aquatic ecosystems, mediating pivotal biogeochemical processes. However, their low abundance in natural environments poses significant challenges for accurate identification and enrichment. Bioelectrochemical systems (BESs) have emerged as a promising tool for enriching EEB from environmental samples, yet the influence of applied potentials on shaping specific EEB populations remains poorly understood. Here, we developed an effective strategy to selectively enrich targeted exoelectrogenic consortia by adapting anode potentials to the redox conditions of paddy soil. Notably, in BESs inoculated with flooded soil, an applied potential of -0.28 V (simulating the redox conditions dominated by iron oxide-hydroxide reduction) preferentially enriched Geobacter-dominated EEB consortia. Metagenomic functional analysis indicated these EEB were primarily engaged in iron respiration. In contrast, drained soil-inoculated BESs required a higher potential (0.33 V, mimicking nitrate-reducing conditions) for optimal enrichment, resulting in Aeromonas as the predominant genus. The enriched community in this scenario exhibited chemoheterotrophic metabolism and nitrate reduction capabilities. The enrichment dynamics underscore how applied potentials modulate both taxonomic composition and functional specialization of EEB along soil redox gradients, with implications for targeted manipulation of microbial communities for environmental biotechnology applications.}, } @article {pmid38695096, year = {2025}, author = {Liu, H and Zhao, X and Xu, S and Zhao, L and Han, X and Xu, X and Zhao, N and Hu, L and Luo, C and Wang, X and Zhang, Q and Guo, T}, title = {Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.}, journal = {Integrative zoology}, volume = {20}, number = {5}, pages = {916-935}, doi = {10.1111/1749-4877.12830}, pmid = {38695096}, issn = {1749-4877}, support = {32100100//Youth Fund Project of National Natural Science Foundation of China/ ; 2022-ZJ-943Q//National Science Foundation of Qinghai Province/ ; LHZX-2022-02//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; China ; *Antelopes/microbiology/physiology ; Sheep/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; *Ruminants/microbiology/physiology ; *Adaptation, Physiological ; Parks, Recreational ; Bacteria/classification/genetics ; Feeding Behavior ; Multiomics ; }, abstract = {The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.}, } @article {pmid40989903, year = {2025}, author = {Malygina, EV and Potapova, NA and Imidoeva, NA and Vavilina, TN and Belyshenko, AY and Morgunova, MM and Dmitrieva, ME and Shelkovnikova, VN and Vlasova, AA and Lipatova, OE and Zhilenkov, VM and Batalova, AA and Stoyanova, EE and Axenov-Gribanov, DV}, title = {Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20037}, pmid = {40989903}, issn = {2167-8359}, mesh = {Russia ; *Microbiota ; *Ascomycota/genetics/classification/isolation & purification ; Symbiosis ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; Mycorrhizae/genetics ; }, abstract = {The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving controlled cultivation. This study aimed to characterize the microbial communities within the surface and gleba of truffle ascomata using 16S and 18S rRNA gene sequencing and identify the taxonomic composition and ecological roles of these microbiota. Specimens of Tuber magnatum (white truffle) and Tuber macrosporum (smooth black truffle) were collected, with T. magnatum representing the first documented discovery of this species in Russia. Metabarcoding profiling identified both species-specific and shared microbial taxa, with the yeast-like fungus Geotrichum spp. emerging as a core symbiont in both truffle species. Its consistent detection in surface and gleba tissues suggests a critical role in mycorrhizal establishment and spore dispersal, potentially mediated by sulfur volatiles that attract mycophagous fauna. In T. magnatum, the bacterial community was dominated by Proteobacteria, particularly Alphaproteobacteria and Gammaproteobacteria, with the nitrogen-fixing genus Bradyrhizobium being especially abundant. The truffle microbiota predominantly comprised soil-derived microorganisms (e.g., nitrogen-fixing Rhizobiaceae spp., phenol-degrading Mycoplana spp.) and plant-associated symbionts (e.g., ectomycorrhizal Sebacina spp.), implicating these communities in nutrient cycling, xenobiotic degradation, and host plant interactions. By elucidating the taxonomic and functional profiles of truffle-associated microbiota, this study provides foundational insights into their ecological contributions. Chemical differences align with tissue-specific microbial communities, suggesting microenvironmental specialization in bioactive compound synthesis. These findings advance efforts to replicate critical symbiotic interactions in vitro, a prerequisite for developing sustainable cultivation protocols for T. magnatum and T. macrosporum under controlled conditions.}, } @article {pmid40988537, year = {2025}, author = {Tsamadou, V and Ohlsson, JA and Schnürer, A}, title = {Converge or Diverge? Exploring the Fate of Taxonomically Different Anaerobic Digestion Communities Under Uniform Growth Conditions.}, journal = {Microbial biotechnology}, volume = {18}, number = {9}, pages = {e70233}, doi = {10.1111/1751-7915.70233}, pmid = {40988537}, issn = {1751-7915}, support = {310432//Energimyndigheten/ ; //Swedish Research Council (VR). The grant agreement corresponds to the Swedish Research Council./ ; //Sveriges Lantbruksuniversitet/Swedish University of Agricultural Sciencesarch Council through grant agreement no. 2022-06725/ ; }, mesh = {Anaerobiosis ; Culture Media/chemistry ; *Bacteria/classification/genetics/metabolism/growth & development ; Sewage/microbiology ; Ammonia/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bioreactors/microbiology ; Biofuels ; DNA, Ribosomal/chemistry/genetics ; *Biota ; Sequence Analysis, DNA ; Metagenomics ; }, abstract = {Biogas inocula with distinct taxonomic compositions often converge to similar communities when fed the same substrate, indicating strong substrate-driven deterministic assembly. Nevertheless, stochastic processes have also been suggested as a critical element for microbial assembly in biogas systems. To date, assembly processes have mainly been investigated with undefined, non-sterile substrates, making it difficult to exclude the influence of external microorganisms. The aim of the present study was to investigate whether three taxonomically distinct anaerobic digestion (AD) communities would converge when exposed to uniform growth conditions during semi-continuous operation with a sterilised defined medium. The inocula originated from mesophilic processes using different substrates (food waste, sludge, and manure) and total ammonia levels (0.5-7.2 g/L). The medium was formulated to support all four main metabolic steps of AD: hydrolysis, fermentation, anaerobic oxidation, and methanogenesis. Taxonomic, phylogenetic, and functional analyses conducted via 16S and metagenomic sequencing showed that the substrate had no deterministic effect on microbial community taxonomic composition. Instead, the final community structure was dictated primarily by the initial inoculum, regardless of changes in substrate composition or ammonia levels. Despite taxonomic divergence, broad-level functionality and operational performance remained similar between communities.}, } @article {pmid40983948, year = {2025}, author = {Zafeiropoulos, H and Delopoulos, EIM and Erega, A and Schneider, A and Geirnaert, A and Morris, J and Faust, K}, title = {microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {292}, pmid = {40983948}, issn = {1474-760X}, support = {101000309//Horizon 2020/ ; 101000309//Horizon 2020/ ; 9017//EMBO Scientific Exchange Grant/ ; }, mesh = {*Software ; *Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Metagenome ; Databases, Genetic ; *Microbiota ; }, abstract = {Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 annotated representative genomes. microbetag can be applied to custom (metagenome-assembled) genomes via its stand-alone version. MGG, a Cytoscape app designed to support microbetag, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.}, } @article {pmid40945093, year = {2025}, author = {Niu, Y and Zhang, X and Jiao, M and Storey, KB and Shekhovtsov, SV}, title = {Metabolic plasticity and gut microbiome synergy underlie high-altitude adaptation in the plateau frog Rana kukunoris: A multi-omics perspective.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {119050}, doi = {10.1016/j.ecoenv.2025.119050}, pmid = {40945093}, issn = {1090-2414}, mesh = {Animals ; *Altitude ; *Gastrointestinal Microbiome/physiology ; *Ranidae/physiology/microbiology/metabolism ; *Adaptation, Physiological ; Metabolomics ; Liver/metabolism ; Acclimatization ; Muscle, Skeletal/metabolism ; Metabolome ; Multiomics ; }, abstract = {Life on the Qinghai-Tibet Plateau is exposed to extreme abiotic stressors, yet endemic frog species such as Rana kukunoris thrive due to specialized adaptations. However, the metabolic and gut microbial mechanisms that enable survival at high altitude remain unclear. Here, we used metabolomic analysis and metagenomic sequencing to compare metabolic profiles of liver and skeletal muscle, as well as gut microbial composition and function, between high- (3730 m) and low-altitude (1990 m) populations. Metabolomic profiling revealed significant altitude-driven shifts, including the down-regulation of glycolysis (fructose-1,6-bisphosphate and glyceraldehyde 3-phosphate decreased by 44.2 % and 40.7 %, respectively) and tricarboxylic acid (TCA) cycle intermediates (fumaric acid and malic acid reduced by 37.7 % and 35.9 %, respectively) in the liver, and enhanced oxidative phosphorylation efficiency via elevated flavins (flavin mononucleotide and flavin adenine dinucleotide increased 1.43- and 1.28-fold, respectively) in skeletal muscle. These findings suggest a conserved strategy of metabolic rate depression and tissue-specific metabolic regulation. Significantly differential metabolites were enriched in glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis, highlighting membrane remodeling as a key adaptive response to cold stress at high altitudes. Moreover, gut microbiomes of high-altitude frogs exhibited increased α-diversity and functional enrichment in the biosynthesis of secondary metabolites, cofactors, amino acids, and carbohydrate-active enzymes (GHs/GTs), all likely improving tolerance to stressful environments and maintaining homeostasis. Key microbial taxa, including Candidatus Udaeobacter, Desulfovibrio, Bradyrhizobium, and Akkermansia, showed a specific dominance in high-altitude frogs, which may support host energy homeostasis and fortify gut barrier function. Multi-omics data highlighted the convergence of protective mechanisms in high-altitude frogs, including autophagy and two-component/quorum sensing systems. This study reveals significant adaptive remodeling of metabolism and gut microbiota in high-altitude R. kukunoris, providing novel insights into host-microbe synergistic interactions under extreme environments.}, } @article {pmid40845638, year = {2025}, author = {Bai, X and Bi, J and Li, A and Zhu, X and Zhao, Z and Hu, H and Pan, H}, title = {Phylosymbiosis of antibiotic resistance genes in pig feces and potential transmission to piggery workers.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118907}, doi = {10.1016/j.ecoenv.2025.118907}, pmid = {40845638}, issn = {1090-2414}, mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Phylogeny ; *Symbiosis ; Humans ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Animal feces are recognized as reservoirs of antibiotic resistance genes (ARGs) that threaten public health and environmental safety. However, it remains unclear whether livestock breeds affect ARGs in feces and how they are transferred from animals to workers. Here, an approach integrated with metagenomics and whole-genome resequencing was used to study Saba (SB) and Large White (LW) pigs on the same pig farm. Higher abundance of both gut bacterial and viral communities and lower abundance of tetracycline and aminoglycoside resistance genes were observed in SB pigs. Gut bacterial communities control the shape of the antibiotic resistome in pig feces. The co-occurrence network showed a close association between ARGs, mobile genetic elements, and gut microbiota in SB pigs. By integrating whole-genome resequencing, an apparent phylosymbiosis was revealed in the antibiotic resistome in pig feces. The structural equation model revealed that host phylogeny primarily directly controlled the antibiotic resistome in pig feces, with additional indirect effects mediated by gut bacterial communities. The flow of ARGs, including pig feces, sludge, flies, and worker feces, between pig farms was further investigated. The findings revealed a direct contribution of pig feces to the ARGs in worker feces, while flies played only a minor role in the transfer of ARGs to pig workers. These findings are essential for developing effective measures to combat antimicrobial resistance in pigs and potential threats to public health.}, } @article {pmid40784097, year = {2025}, author = {Lin, Y and Wang, X and Zhao, D and Zhou, H and Wang, Y and Gao, Y and Lin, Y and Xu, G and Ni, K and Yang, F}, title = {Waterlogging-induced restructuring of phyllosphere microbiota associated with mycotoxin accumulation.}, journal = {Ecotoxicology and environmental safety}, volume = {303}, number = {}, pages = {118821}, doi = {10.1016/j.ecoenv.2025.118821}, pmid = {40784097}, issn = {1090-2414}, mesh = {*Zea mays/microbiology ; Plant Leaves/microbiology ; *Microbiota ; *Mycotoxins/metabolism ; Fungi/genetics ; }, abstract = {As waterlogging events intensify and become more frequent in the future, understanding their impact on plant physiology and associated microbes is crucial for alleviating stress in vulnerable species and ecosystems. Despite its importance, our understanding of how phyllosphere microbiota react to waterlogging stress remains limited. This study utilized metagenomic sequencing to assess the effects of waterlogging on microbial diversity and functional activities in different tissues of the maize phyllosphere, focusing specifically on leaves and ears. Our findings indicated that waterlogging significantly affected the maize phyllosphere microbial communities. Also, waterlogging altered the microbial interaction networks by increasing network complexity, enhancing negative interactions, and shifting the relative abundance of key bacterial and fungal genera. Moreover, metagenomic analysis revealed upregulated signaling pathways and oxidative stress responses, particularly within the fungal communities associated with maize ears. Crucially, we identified a higher abundance of genes related to mycotoxin production under waterlogged conditions, leading to elevated mycotoxin levels in ear tissues. These results suggest that waterlogging-induced changes in fungal communities may heighten the risk of mycotoxin contamination in maize. The distinct microbial responses noted between maize leaves and ears further highlight the tissue-specific dynamics of these communities.}, } @article {pmid40752224, year = {2025}, author = {Carrillo-Barragán, P and Cassola, GE and Burkhardt-Holm, P}, title = {Microbial colonisation of polyethylene in offshore marine environments: Insights from the Southern and South Atlantic Oceans.}, journal = {The Science of the total environment}, volume = {996}, number = {}, pages = {180189}, doi = {10.1016/j.scitotenv.2025.180189}, pmid = {40752224}, issn = {1879-1026}, mesh = {*Polyethylene/analysis/metabolism ; Atlantic Ocean ; RNA, Ribosomal, 16S/analysis ; Seawater/microbiology ; *Water Pollutants, Chemical/analysis/metabolism ; *Microbiota ; Bacteria ; }, abstract = {Plastic debris is a pervasive environmental pollutant, with polyethylene (PE) among the most abundant floating polymers in marine environments. While microbial colonisation of marine plastics has been extensively documented, most studies focus on coastal waters in the Northern Hemisphere, leaving colonisation dynamics in remote Southern Hemisphere regions poorly understood. Here, we investigate early microbial colonisation of PE films incubated during two oceanographic transects across the Southern Ocean and South Atlantic Ocean. Using 16S rRNA gene amplicon sequencing and shotgun metagenomics, we assessed how geographic location, incubation regime (aquarium vs ship deck), and environmental factors (UV exposure, temperature, and salinity) shape microbial community structure and functional potential. Community composition was primarily influenced by transect location and incubation conditions, rather than material type. Dominant taxa included Cyanobacteria, Pseudomonadota, and Bacteroidota, taxa often associated with phototrophy, hydrocarbon degradation, and early surface colonisation. Functional analyses revealed enrichment in pathways related to biofilm formation, hydrocarbon degradation, lipid oxidation, and iron metabolism. These findings highlight how environmental conditions shape early plastisphere assembly and metabolic capabilities in understudied oceanic regions of the Southern Hemisphere.}, } @article {pmid40982389, year = {2025}, author = {Pizzini, JD and Midani, FS and Britton, RA}, title = {Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA).}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {223}, pages = {}, doi = {10.3791/68788}, pmid = {40982389}, issn = {1940-087X}, mesh = {*Bioreactors/microbiology ; *Microbiota/physiology ; Humans ; }, abstract = {The human microbiome comprises diverse and dynamic microbial communities that play essential roles in host health. Understanding these communities and their responses to environmental factors is critical for advancing microbiome-based therapeutics. Traditional in vitro models for cultivating human-derived microbiota often lack scalability and require extensive technical expertise, limiting their accessibility and throughput. To address these limitations, we developed the Minibioreactor Array (MBRA) system -- a modular, single-stage, continuous-flow platform for high-throughput cultivation of microbial communities. This system enables parallel cultivation of up to 48 distinct microbial communities, supporting experimental flexibility while maintaining the stable growth of complex ecosystems. This protocol provides detailed guidance on MBRA fabrication, assembly, sterilization, and operation. The system's modular design allows for easy integration into anaerobic chambers and supports customization for a wide range of experimental applications. It has been used to study microbial responses to antibiotics, dietary compounds, and pathogen invasion, and to screen for pathogen-resistant communities. With its accessibility, scalability, and reproducibility, the MBRA represents a powerful model system for investigating microbial interactions and advancing microbiome research.}, } @article {pmid40929881, year = {2025}, author = {Liu, Y and Li, K and Xu, J and Shen, W and Li, Y and Ma, J and Wang, T and Liu, J and Li, T and Zhang, X and Tian, W and Tian, J and Wang, H and Zhang, X}, title = {Alpha-linolenic acid ameliorates T2DM via reshaping gut-liver axis and inflammatory GPR120-NF-κB/NLRP3 pathway in mouse and rat models.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {147}, number = {}, pages = {157214}, doi = {10.1016/j.phymed.2025.157214}, pmid = {40929881}, issn = {1618-095X}, mesh = {Animals ; *alpha-Linolenic Acid/pharmacology ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Liver/drug effects/metabolism ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; NF-kappa B/metabolism ; Rats ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Insulin Resistance ; Inflammation/drug therapy ; }, abstract = {BACKGROUND: The gut-liver axis, pivotal in managing glucose balance and insulin responsiveness, is central to the development of type 2 diabetes mellitus (T2DM). Research has highlighted the regulatory effects of dietary alpha-linolenic acid (ALA), but it remains unclear how ALA modulates gut microbiota and liver inflammation in T2DM.

PURPOSE: This study aimed to systematically investigate ALA's influence on liver inflammation, intestinal barrier integrity, gut microbial composition, and metabolic homeostasis in T2DM, with a focus on the underlying molecular mechanisms.

STUDY DESIGN: A dual-model approach was employed using both db/db mouse model and the SCZ/NA-induced T2DM rat model to ensure robust species and model validation.

METHODS: Animals received oral ALA supplementation, followed by assessments of glucose tolerance, insulin sensitivity, hepatic histology, and inflammatory markers. Intestinal barrier function, permeability, and systemic LPS levels were evaluated. Mechanistic analysis focused on the GPR120-NF-κB/NLRP3 signaling pathway. Multi-omics profiling including fecal metagenomics, SCFA quantification, and plasma metabolomics were conducted to assess gut microbiota and host metabolic responses.

RESULTS: Our results revealed that ALA therapy significantly mitigated insulin resistance and glucose intolerance in db/db mice. Histopathological analysis revealed a decrease in hepatic steatosis following ALA administration, alongside a reduction in inflammatory markers indicative of T2DM. Importantly, our findings demonstrated that ALA mitigates liver inflammation by inhibiting the NF-κB/NLRP3 pathway, possibly via its interaction with GPR120. Beyond this, augmenting ALA bolstered intestinal integrity, minimized permeability, curbed lipopolysaccharide leakage, and suppressed pro-inflammatory cytokine expression within the intestines. Significantly, an integrated multi-omics investigation, encompassing fecal metagenomic sequencing, SCFA evaluation, and plasma non-targeted metabolomics, disclosed a potent correlation between ALA's hypoglycemic efficacy and the modulation of gut microbial community structure, elevation of SCFA synthesis, and enhancement of metabolic signatures.

CONCLUSION: Our study's initial insights indicated that dietary ALA modulates inflammation and metabolism in T2DM via the gut-liver axis, specifically through the GPR120-NF-κB/NLRP3 pathway. This elucidates ALA's dual function in reshaping the gut microbiota and combating systemic inflammation, positioning it as a potentially efficacious dietary component for managing T2DM.}, } @article {pmid40911291, year = {2025}, author = {Zhang, G and Yue, Y and Tu, L and Liu, Q and Zhang, Q and Shang, K}, title = {Responses of microbial communities during oilseed plant-based phytoremediation of heavy metal-contaminated soils.}, journal = {Journal of applied microbiology}, volume = {136}, number = {9}, pages = {}, doi = {10.1093/jambio/lxaf226}, pmid = {40911291}, issn = {1365-2672}, support = {G222408//Shanghai Landscaping and City Appearance Administration Bureau/ ; }, mesh = {Biodegradation, Environmental ; *Metals, Heavy/metabolism/analysis ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; Fungi/genetics/metabolism/isolation & purification/classification ; Bacteria/genetics/classification/metabolism/isolation & purification ; Archaea/genetics/metabolism/isolation & purification/classification ; *Microbiota ; Soil/chemistry ; }, abstract = {AIMS: Phytoremediation is an effective method of remediating soils contaminated with heavy metals. However, it has some limitations in practical applications with regard to rare plant species, poor environmental adaptability, and long growth cycles. The dynamic response mechanisms of soil microbial communities during phytoremediation are still unclear, which restricts the optimization and promotion of this approach.

METHODS AND RESULTS: No ethical approval was required for this study. In this study, soil bacterial, fungal, and archaeal communities during the remediation of Cu-, Pb-, and Zn-contaminated soils with five industrial oilseed plants [Xanthium strumarium (XS), Bidens pilosa (BP), Kosteletzkya virginica (KV), Sesbania cannabina (SC), and Commelina communis (CC)] were analyzed using metagenome sequencing. Compared with soil contaminated with heavy metals, remediation through five industrial oilseed plants significantly reduced the content of heavy metals in the soil, with soil Cu, Pb, and Zn decreasing by 44.01%, 46.32%, and 27.62%, respectively, and WSCu, WSPb, and WSZn content decreasing by 28.23%, 50.68%, and 75.26%, respectively. Microbial diversity analysis showed that the phytoremediation significantly affected the soil microbial communities, with a significant decrease in archaeal diversity. Variation partitioning analysis and Mantel tests revealed that heavy metals and soil physicochemical properties significantly affected microbial communities, and heavy metals exerted stronger effects on archaeal communities. Meanwhile, soil contaminated with heavy metals was mainly dominated by fungal-fungal interactions, whereas phytoremediation increased the complexity of microbial symbiotic networks.

CONCLUSION: Collectively, these results provide fundamental insights into the microbial community structure during phytoremediation of heavy metal-contaminated soil, which may aid in the bioregulation of phytoremediation.}, } @article {pmid40857949, year = {2025}, author = {Jin, L and Yuan, L and Bürgmann, H and Ju, F}, title = {Wastewater treatment plant effluent drives coupled changes of viral and bacterial community structure and function in impacted rivers.}, journal = {Environment international}, volume = {203}, number = {}, pages = {109737}, doi = {10.1016/j.envint.2025.109737}, pmid = {40857949}, issn = {1873-6750}, mesh = {*Rivers/microbiology/virology ; *Wastewater/microbiology/virology ; *Bacteria/classification ; *Waste Disposal, Fluid ; Viruses/classification ; *Water Microbiology ; Microbiota ; }, abstract = {The discharge of wastewater treatment plant (WWTP) effluent containing bacteria and viruses has significant ecological and public health implications for aquatic ecosystems. While viruses infecting bacterial hosts are abundant and diverse in wastewater, their environmental fate, host association, and functional impact in affected river ecosystems remain poorly understood. Using a metagenomic approach, we characterized double-stranded DNA viral communities across nine WWTPs and impacted riverine habitats, including water, suspended particles, sediment, and epilithic biofilm. River water was the most affected habitat by WWTP effluent, with viral diversity increasing by 22 % (±15 %) downstream. In contrast, no significant differences were observed in either viral or bacterial community structures across locations in biofilm or sediment. Among 38,826 viral operational taxonomic units (vOTUs) recovered from 148 metagenomes, 18 % were shared exclusively between effluent and downstream habitats, primarily with river water (99 % of the vOTUs). These wastewater-associated vOTUs were predicted to infect key bacterial taxa involved in carbon and nitrogen cycling (e.g., Nitrosomonas and Methylomonadaceae) and potential human pathogens (e.g., Vibrio and Ralstonia). Additionally, WWTP effluent increased the diversity of virus-encoded auxiliary metabolic genes, especially those involved in carbon, nutrient, and drug metabolism, suggesting potential roles in shaping host fitness and environmental adaptation. Overall, our findings demonstrate that WWTP effluent drives coupled changes in viral and bacterial communities in river water, highlighting the potential ecological consequences of virus-host interactions in wastewater-impacted aquatic environments.}, } @article {pmid40827925, year = {2025}, author = {Caffrey, EB and Olm, MR and Kothe, CI and Wastyk, HC and Evans, JD and Sonnenburg, JL}, title = {MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics.}, journal = {mSystems}, volume = {10}, number = {9}, pages = {e0014125}, doi = {10.1128/msystems.00141-25}, pmid = {40827925}, issn = {2379-5077}, support = {R01-DK085025//Bill and Melinda Gates Foundation/ ; F32-DK128865//U.S. Department of Health and Human Services/ ; NNF20CC0035580//Novo Nordisk/ ; }, mesh = {*Metagenomics/methods ; *Fermented Foods/microbiology ; *Food Microbiology/methods ; Workflow ; Fermentation ; Microbiota/genetics ; Metagenome ; Humans ; Bacteria/genetics/classification ; }, abstract = {Fermented foods, which contain a diversity of microbes and microbial metabolites, have been used for millennia to increase food security, flavor, and nutritional content; more recently, they have been recognized as potential mediators of human health. Metagenomics is a powerful approach to characterize microbes in fermented foods, providing high taxonomic resolution and functional insights. Here, we introduce the Microbial Food DataBase, a metagenomics-based approach designed for the identification of fermentation-associated microbes. Using this primary database of metagenome-assembled genomes and relevant deposited genomes of prokaryotes, eukaryotes, and common food-relevant substrates, we investigated 89 fermented food samples. We present a streamlined high-confidence characterization of microbial diversity in fermented food, identifying previously undiscovered genomes and facilitating strain-level tracking across food environments. The easy and robust functionality of the workflow has significant implications for advancing food safety, promoting desired microbial communities, and increasing sustainability in food production.IMPORTANCEFermented foods have microbial communities that influence food safety, flavor, and human health. Microbial Food DataBase (MiFoDB), an alignment-based sequencing workflow and database, addresses the limitations of existing tools by enabling strain-level resolution, identifying novel genomes, and providing functional insights into microbial communities. Applying MiFoDB to fermented food samples, we demonstrate its ability to uncover novel species, track microbial strains across substrates, and integrate functional annotations. Additionally, the outlined workflow is highly customizable and can be used to generate alignment-based databases for other microbial ecosystems. This work highlights the importance of fermentation-specific workflows for studying microbial food ecosystems, advancing food safety, sustainability, and innovation in fermented food research.}, } @article {pmid40827869, year = {2025}, author = {Allen, JM}, title = {Rediscovering the wild: MiFoDB brings fermented food microbiomes into focus.}, journal = {mSystems}, volume = {10}, number = {9}, pages = {e0059925}, doi = {10.1128/msystems.00599-25}, pmid = {40827869}, issn = {2379-5077}, mesh = {Humans ; *Fermented Foods/microbiology ; *Microbiota/genetics ; *Food Microbiology/methods ; *Metagenomics/methods ; Fermentation ; }, abstract = {Fermented foods have sustained human societies for thousands of years, with their microbial communities subtly shaping flavor, nutrient preservation, and health. Yet despite this long-standing relationship, much of the microbial complexity within fermented foods remains unresolved. In recent work, Caffrey et al. (E. B. Caffrey, M. R. Olm, C. I. Kothe, H. C. Wastyk, et al., mSystems 10:e00141-25, 2025, https://doi.org/10.1128/msystems.00141-25) put forth a new tool, MiFoDB, a metagenomic workflow that offers a promising alternative for advancing food microbiome science. By enabling strain-level resolution, functional gene annotation, and microbial tracking across substrates and time, MiFoDB provides a clearer view into the ecological and functional landscape of the fermented food microbiota. This work also bridges gaps between food and human microbiome research and brings us closer to a mechanistic understanding of how fermented foods influence health, helping transform ancient dietary practices into actionable and targeted nutritional strategies for improving human health and well-being.}, } @article {pmid40815468, year = {2025}, author = {Gao, Y and Wang, D and Lu, T and Liu, K and Li, S and Kang, J and Sha, S and Xing, G and Cheng, L and Fan, S and Yang, W and Yan, Q and Ding, Y and Xu, D}, title = {Cross-cohort microbiome-wide study reveals consistent alterations in the gut bacteriome, but not the gut mycobiome, in patients with hypertension.}, journal = {mSystems}, volume = {10}, number = {9}, pages = {e0065725}, doi = {10.1128/msystems.00657-25}, pmid = {40815468}, issn = {2379-5077}, support = {82370563//National Natural Science Foundation of China/ ; 2021024//Dalian Municipal Dengfeng Clinical Medicine Grant Support/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Hypertension/microbiology ; Middle Aged ; *Mycobiome ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Aged ; Fungi/classification/genetics ; Cohort Studies ; Adult ; Case-Control Studies ; }, abstract = {UNLABELLED: Hypertension, one of the most prevalent cardiovascular diseases, has been linked to the gut microbiota. However, there is a lack of well-defined, cross-population validated gut microbial signatures associated with hypertension, particularly at both the bacterial and fungal levels. To address this gap, we conducted a metagenome-wide analysis of fecal samples from 159 hypertensive patients and 101 healthy controls, using two publicly available data sets from the Beijing and Dalian regions. Our results showed that hypertensive patients exhibit a significant reduction in gut bacterial diversity, accompanied by substantial alterations in bacterial composition. A total of 61 bacterial species were identified with significantly different relative abundance between patients and controls across both regions (combined P < 0.05, q = 0.25). Hypertension-enriched species included Lachnospiraceae (Clostridium symbiosum, Enterocloster bolteae) and Clostridium sp. AT4, while Lachnospiraceae bacterium, Firmicutes bacterium, and Clostridium sp. AM49 4BH were significantly decreased in hypertensive patients. In contrast, no significant differences were observed in gut fungal diversity between hypertensive patients and healthy controls, and only minor differences in fungal composition were noted. Specifically, six fungal species were identified as potentially significant in the combined data set (P < 0.05, q = 0.73), but they only Blastomyces emzantsi c231 meet the same consistency across the two cohorts as the bacterial signatures. Furthermore, we developed classification models using gut bacterial and fungal signatures to distinguish hypertension patients from healthy controls. The bacterium-based models achieved area under the curves (AUCs) greater than 0.70 in cross-cohort classification and validation, while the fungus-based models only achieved AUCs between 0.55 and 0.57. In summary, our study identifies cross-cohort gut bacterial and fungal signatures associated with hypertension, suggesting that the gut bacteriome may serve as a more reliable target for hypertension intervention compared to the gut mycobiome.

IMPORTANCE: Hypertension (HTN) represents a global health burden affecting billions of individuals worldwide; however, the relationship between HTN and gut microbial ecosystems remains inadequately characterized. This study presents the first cross-cohort microbiome analysis revealing significant alterations in the gut bacteriome of HTN patients, with limited changes observed in the mycobiome. These findings highlight the critical role of the gut bacteriome in the pathogenesis of HTN and provide new microbial biomarkers for early diagnosis. Furthermore, the identification of bacterial species establishes a foundation for future intervention approaches, enhancing the applicability of microbiome research in cardiovascular health and opening new avenues for related studies in this field.}, } @article {pmid40803594, year = {2025}, author = {Wenderlein, J and Burkhardt, W and Dietrich, S and Trefflich, I and Penczynski, K and Thomas, K and Salzinger, C and Abraham, K and Malorny, B and Weikert, C and Ansorge, R and Grützke, J}, title = {Beyond the plate: A pilot study exploring the microbial landscape of omnivores and vegans through 16S rRNA gene amplicon sequencing and metagenomics.}, journal = {Clinical nutrition ESPEN}, volume = {69}, number = {}, pages = {551-565}, doi = {10.1016/j.clnesp.2025.08.008}, pmid = {40803594}, issn = {2405-4577}, mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Male ; Female ; Adult ; *Vegans ; Middle Aged ; *Diet, Vegan ; Diet ; Diet, Vegetarian ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND & AIMS: Previous studies have described benefits and risks on human health associated with a vegan diet. Although it is recognized that diet affects the gut microbiota, there is no consensus on the effects of a vegan diet compared to omnivorous diet on the gut microbiota. We have conducted a pilot study to assess the differences between the gut microbiome of vegans and omnivores in 2017 and 2021.

METHODS: Fecal samples of 23 vegans and 23 omnivores (n = 46) were collected in 2017 and 2021 together with more than 300 dietary, lifestyle, and health related characteristics. The fecal microbiome was assessed comparing both amplicon sequencing and metagenome sequencing, to determine robust signals agnostic of sequencing approaches.

RESULTS: Dietary grouping itself explained a small (∼4 %) but significant proportion of the individual variation between microbiota. Natural clustering of microbiomes explained an even larger proportion. We found Ruminococcus torques to be relatively enriched in omnivores compared to vegans across methods and years. Interestingly, this species has been previously associated with unfavorable health outcomes. Despite a low sample size, we found some consistent differences between microbiota of individuals consuming either a vegan or omnivorous diet.

CONCLUSIONS: These results were consistent with recently published gut microbiome signatures of vegans and omnivores across three different countries. Therefore, this small dataset allows a first insight into the gut microbiota of another county's omnivores and vegans whereby detailed and relevant dietary, lifestyle and health related characteristics collected in this study aid in understanding of the connection between respective diets and the microbiome.}, } @article {pmid40772734, year = {2025}, author = {Wei, Z and Meng, L and Du, S and Wang, F and Jiang, A and Lu, R and Liu, K and Wang, X and Xu, Q and Mu, X and Meng, L and Shao, C}, title = {Metabolic potentials of the gut microbes in Antarctic krill (Euphausia superba).}, journal = {mSystems}, volume = {10}, number = {9}, pages = {e0037725}, doi = {10.1128/msystems.00377-25}, pmid = {40772734}, issn = {2379-5077}, support = {4240060500//National Science Foundation for Young Scientists of China/ ; 2022YFC2807505//National Key Research and Development Program of China/ ; ZR2024QD165//National Science Foundation for Young Scientists of Shandong, China/ ; 2023TD19//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 2022QNLM030004//Marine S&T Fund of Shandong Province for Pilot National Laboratary for Marine Science and Technology (Qingdao)/ ; ZDKC-2022-03//Technological Innovation Projects of Qingdao West New Area/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Euphausiacea/microbiology/metabolism ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenome ; Metagenomics/methods ; Bacteria/metabolism/genetics/classification ; }, abstract = {Antarctic krill (Euphausia superba) plays crucial roles in the Southern Ocean biological system, yet the ecological functions of their gut microbiota remain poorly understood. The study investigated the composition and diversity of the gut microbiota in E. superba using 16S rRNA gene sequencing, revealing a highly diverse and tissue-specific microbiota. Further investigation through direct metagenomics and culture-enriched metagenomics identified 12 metagenome-assembled genomes (MAGs), which might represent novel species based on their phylogenetic positions, average nucleotide identity (ANI), average amino acid identity (AAI), and relative evolutionary divergence (RED) values. These MAGs were grouped into two distinct clusters according to their completeness of metabolic modules. Although MAGs in cluster 2 showed lower read relative abundance compared to those in cluster 1, they exhibited a greater number of amino acid synthesis modules. The synthesis of glutathione, heme, ubiquinone, vitamins, and betaine by MAGs suggested potential roles in enhancing survival of E. superba in extreme environment. Moreover, the functional genes in the 12 MAGs had abundant transcripts indicating they exhibited high metabolic activity in the E. superba gut microbiota. These findings shed new light on the metabolic contributions of gut microbiota in E. superba.IMPORTANCEThis study provided a comprehensive characterization of the gut microbiome of Euphausia superba, revealing its diverse and functionally distinct microbial community. Furthermore, 12 metagenome-assembled genomes (MAGs) representing novel species were successfully identified. The metabolic analysis demonstrated that these microbes contribute to host nutrient acquisition by synthesizing essential amino acids and vitamins. The identification of antioxidant and osmoregulatory compound synthesis modules suggested that gut microbiota might facilitate the survival of E. superba in the harsh Antarctic environment. Those findings elucidated the host-microbe interactions in polar marine ecosystems and provided new insights into microbial contributions to host nutrient cycling and environmental adaptation in the Southern Ocean.}, } @article {pmid40583454, year = {2025}, author = {Aldrian, D and Pollio, A and Mayerhofer, C and Diederen, K and Jacobs, JP and Pai, N and Szamosi, JC and Hart, L and Turner, D and Del Chierico, F and Cardile, S and Grigoryan, Z and Chen, LA and Hurych, J and Cinek, O and Taddei, CR and Schwerd, T and Wine, E and Griffiths, AM and Müller, T and Vogel, GF}, title = {Fecal Microbial Community Profiling Allows Discrimination of Phenotype and Treatment Response in Pediatric Crohn's Disease and Ulcerative Colitis-An International Meta-Analysis.}, journal = {Inflammatory bowel diseases}, volume = {31}, number = {9}, pages = {2338-2351}, doi = {10.1093/ibd/izaf135}, pmid = {40583454}, issn = {1536-4844}, mesh = {Humans ; *Crohn Disease/microbiology/drug therapy ; *Colitis, Ulcerative/microbiology/drug therapy ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Phenotype ; Male ; Female ; Biomarkers/analysis ; RNA, Ribosomal, 16S/genetics ; Adolescent ; }, abstract = {BACKGROUND AND AIMS: The pathophysiology of pediatric inflammatory bowel disease (PIBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is not entirely understood. Dysregulation of the intestinal microbiome is recognized as both a disease-driving and a potential therapeutic target. This study aimed to systematically analyze gut microbiome compositions and its applicability as a biomarker for disease progress and treatment response.

METHODS: Bibliographic and nucleotide databases were searched. Raw 16S-rRNA sequencing reads were subjected to a uniform downstream dada2/phyloseq pipeline to extract taxonomy, community structure, and abundance information. Patient metadata were extracted from publications, and study authors were contacted for further details if required.

RESULTS: Twenty-six studies comprising 3956 stool samples (CD 41%, UC 36%, 23% healthy) were included in the analyses. Median age of individuals was 12 (interquartile range 4). Sex distribution was comparable. Alpha diversity was reduced between the healthy and both UC and CD treatment-naïve groups (P < .001) and further reduced with increasing clinical disease activity. Beta diversity revealed altered community structure in treatment-naïve children with PIBD (P < .001). This alteration remained in patients in clinical remission (P < .001). Machine learning models discriminated between treatment-naïve patients with CD or UC with an area under the receiver operating characteristics curve (AUROC) of 98%. Microbial communities differed between patient responders versus nonresponders to treatment (P < .001). Further, microbial community profiling distinguished treatment response (eg, steroid, nutrition, or TNFα) with AUROCs of 82%-90%.

CONCLUSIONS: Gut microbial community structure is substantially altered in active and inactive PIBD and may be utilized as a biomarker for differentiating PIBD subtype and predicting treatment response.}, } @article {pmid40556523, year = {2025}, author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E}, title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.}, journal = {Inflammatory bowel diseases}, volume = {31}, number = {9}, pages = {2521-2534}, doi = {10.1093/ibd/izaf089}, pmid = {40556523}, issn = {1536-4844}, support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; }, mesh = {Animals ; *Colitis/chemically induced/immunology/pathology/microbiology ; *Gastrointestinal Microbiome/immunology ; Dextran Sulfate/toxicity ; Mice ; Mice, Knockout ; *Germinal Center/immunology ; Disease Models, Animal ; Mice, Inbred C57BL ; *Trans-Activators/deficiency/physiology ; Th17 Cells/immunology ; }, abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.

METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.

RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA⁺ plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.

DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.}, } @article {pmid40544449, year = {2025}, author = {Yew, WC and Young, GR and Cheung, W and Nelson, A and Berrington, JE and Smith, DL}, title = {Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk.}, journal = {STAR protocols}, volume = {6}, number = {3}, pages = {103917}, pmid = {40544449}, issn = {2666-1667}, mesh = {*Milk, Human/chemistry/virology/metabolism ; Humans ; *Lipidomics/methods ; *Bacteriophages/genetics ; Infant, Newborn ; Infant, Premature ; Metagenomics/methods ; *Lipids/analysis ; Female ; *Virome ; Computational Biology/methods ; }, abstract = {Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.[1].}, } @article {pmid40387216, year = {2025}, author = {Steriade, C and Thomas, SC and Xu, F and Ahituv, A and Hanin, A and Pleshkevich, M and Hwang, S and Ramirez, A and Foreman, B and Yoo, JY and Eka, O and Kellogg, M and Oliger, A and Wainwright, MS and Morales, M and Gaspard, N and Hirsch, LJ and Devinsky, O and Saxena, D}, title = {Patients with status epilepticus and new-onset refractory status epilepticus display drastically altered fecal microbiomes compared to chronic epilepsy patients.}, journal = {Epilepsia}, volume = {66}, number = {9}, pages = {3254-3268}, doi = {10.1111/epi.18450}, pmid = {40387216}, issn = {1528-1167}, support = {//NORSE Institute, the Daniel Raymond Wong Memorial Research Fund and CCEMRC/ ; //Parekh Center for Interdiscplinary Neurology/ ; //National Organization for Rare Disorders and American Epilepsy Society/ ; }, mesh = {Humans ; *Status Epilepticus/microbiology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; *Feces/microbiology ; Middle Aged ; Longitudinal Studies ; *Epilepsy/microbiology ; Chronic Disease ; Cohort Studies ; *Drug Resistant Epilepsy/microbiology ; Young Adult ; Cytokines/blood ; Aged ; }, abstract = {OBJECTIVE: New-onset refractory status epilepticus (NORSE) occurs in people without pre-existing epilepsy or a rapidly identified structural, toxic, metabolic, or other cause. NORSE is a rare disorder with high morbidity and mortality rates and limited evidence for effective therapies. We aimed to assess whether the gut microbiome of NORSE and status epilepticus (SE) differs from that of chronic epilepsy, whether NORSE differs from SE at different disease time points, and to examine the correlations between specific gut microbiota and cytokines in NORSE and SE.

METHODS: This longitudinal cohort study observed patients with NORSE (n = 15), SE (n = 17), and chronic epilepsy who were not in SE (n = 12). NORSE patients were recruited through the NORSE Consortium. Patients with NORSE and SE underwent longitudinal serial biospecimen collection. Fecal samples were subjected to whole-community shotgun metagenomics to characterize microbiome features. Cohorts were evaluated for prokaryotic, eukaryotic, and functional diversity. Correlations between blood inflammatory cytokine levels and microbiome features and covariate analysis with critical illness and clinical treatments were examined for NORSE and SE patients during and after SE resolution.

RESULTS: During SE, NORSE and SE patients had significantly different prokaryotic, eukaryotic, and functional microbiome levels compared to chronic epilepsy patients without SE. Limited microbiome differences were observed within and between NORSE and SE, although these groups displayed differing correlation patterns between microbial species and cytokines. Patients who later died or were tube-fed harbored significantly different microbiomes than those who survived or were orally fed.

SIGNIFICANCE: NORSE and SE patients present with a more variable and dramatically different fecal microbiome than chronic epilepsy patients, which may indicate gut dysbiosis that may be reciprocally linked to inflammatory responses. Although NORSE and SE patients had similar microbiome structures, fungal and bacterial correlates with inflammatory cytokines differed between NORSE and SE, with confounding factors influencing microbiome structure. Our data suggest a microbiome-specific response to NORSE and SE, with implications for future treatment strategies.}, } @article {pmid40289407, year = {2025}, author = {Aho, VTE and Clerbaux, LA and Kupczok, A and Tillett, B and Garg, N and Henderickx, JGE}, title = {A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.}, journal = {Proteomics}, volume = {25}, number = {17-18}, pages = {28-32}, doi = {10.1002/pmic.202500019}, pmid = {40289407}, issn = {1615-9861}, mesh = {*Proteomics/methods ; *Microbiota ; Humans ; *Metagenomics/methods ; Metabolomics/methods ; }, abstract = {Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling the function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies of the microbiome, complementing genome-resolved metagenomics, metatranscriptomics, and metabolomics. The potential advancements from metaproteomics and multiomics research touch a breadth of disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, and medicine, and could lead to both fundamental and applied discoveries. However, there are significant roadblocks to widespread adoption of metaproteomics among microbiome researchers. In this Viewpoint article, we highlight the pivotal role of metaproteomics in microbiome research by showcasing its advantages, exploring opportunities to overcome challenges, and paving the way for its broader adoption as a mainstream technique. We hope that the recommendations provided in this Viewpoint article will inspire new, beneficial collaborations between proteomics experts, algorithm and infrastructure developers, biochemists, cell biologists, and microbiologists, enabling the construction of a knowledge base of microbiome function that can have an immediate and direct impact on host health and the environment.}, } @article {pmid39981802, year = {2025}, author = {Bartlett, A and Blakeley-Ruiz, JA and Richie, T and Theriot, CM and Kleiner, M}, title = {Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.}, journal = {Proteomics}, volume = {25}, number = {17-18}, pages = {43-50}, pmid = {39981802}, issn = {1615-9861}, support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; 593607//Foundation for Food and Agriculture Research/ ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; R35GM138362//National Institute of General Medical Sciences of the National Institutes of Health/ ; }, mesh = {Animals ; *Dietary Proteins/analysis ; Mice ; *DNA, Bacterial/analysis/genetics ; *Gastrointestinal Microbiome ; Caseins ; Metagenomics/methods ; Feces/microbiology/chemistry ; *Bacterial Proteins/analysis ; Proteomics/methods ; *Microbiota ; Diet ; Mice, Inbred C57BL ; }, abstract = {Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Defined diets frequently use purified casein as the protein source. Previous work indicated that casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and found that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.}, } @article {pmid39757511, year = {2025}, author = {Tanca, A and Masia, S and Giustacchini, P and Uzzau, S}, title = {Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study.}, journal = {Proteomics}, volume = {25}, number = {17-18}, pages = {62-69}, doi = {10.1002/pmic.202400191}, pmid = {39757511}, issn = {1615-9861}, support = {//Italian MIUR/ ; }, mesh = {*Diet, Ketogenic ; Humans ; *Proteomics/methods ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; Drug Resistant Epilepsy/diet therapy/microbiology ; }, abstract = {Metaproteomics is a valuable approach to characterize the biological functions involved in the gut microbiota (GM) response to dietary interventions. Ketogenic diets (KDs) are very effective in controlling seizure severity and frequency in drug-resistant epilepsy (DRE) and in the weight loss management in obese/overweight individuals. This case study provides proof of concept for the suitability of metaproteomics to monitor changes in taxonomic and functional GM features in an individual on a short-term very low-calorie ketogenic diet (VLCKD, 4 weeks), followed by a low-calorie diet (LCD). A marked increase in Akkermansia and Pseudomonadota was observed during VLCKD and reversed after the partial reintroduction of carbohydrates (LCD), in agreement with the results of previous metagenomic studies. In functional terms, the relative increase in Akkermansia was associated with an increased production of proteins involved in response to stress and biosynthesis of gamma-aminobutyric acid. In addition, VLCKD caused a relative increase in enzymes involved in the synthesis of the beta-ketoacid acetoacetate and of the ketogenic amino acid leucine. Our data support the potential of fecal metaproteomics to investigate the GM-dependent effect of KD as a therapeutic option in obese/overweight individuals and DRE patients.}, } @article {pmid40982108, year = {2025}, author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S}, title = {Demonstrated role of sulfate-reducing bacterial consortia in anaerobic paracetamol biodegradation.}, journal = {Biodegradation}, volume = {36}, number = {5}, pages = {91}, pmid = {40982108}, issn = {1572-9729}, support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST) PURSE Grant, New Delhi, India/ ; }, mesh = {*Acetaminophen/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Sulfates/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics/classification ; *Water Pollutants, Chemical/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The escalating global production and usage of paracetamol (C8H9NO2), a widely administered analgesic and antipyretic pharmaceutical, has led to its ubiquitous presence in environmental matrices, including surface waters, municipal wastewater, and even potable water sources. Owing to its persistence and bioaccumulative potential, paracetamol poses a significant ecotoxicological threat, particularly through trophic transfer in aquatic ecosystems. Conventional wastewater treatment methods often fall short in completely eliminating such micropollutants. In this context, bioremediation offers a promising, sustainable, and cost-effective alternative for pharmaceutical remediation. This study investigates the anaerobic degradation potential of two sulfate-reducing bacterial consortia, designated Consortium I and Consortium II, isolated from Okhla landfill leachate and enriched with distinct Postgate media formulations. Paracetamol was introduced at varying concentrations (50-500 mg/L), with and without supplementation of an auxiliary carbon source, sodium lactate. Metagenomic profiling via 16S rRNA sequencing revealed that Consortium I was primarily composed of Clostridium (40.1%) and Acidipropionibacterium (31.2%), whereas Consortium II exhibited a dominant presence of Clostridium (80.3%) and Bacillus (7.99%). Consortium II exhibited superior degradation kinetics, achieving complete removal of 500 mg/L paracetamol in 48 h under lactate-free conditions. Conversely, the presence of sodium lactate significantly attenuated degradation efficiency, suggesting substrate competition and metabolic preference. Gas chromatography-mass spectrometry (GC-MS) identified 4-aminophenol and hydroquinone as transient intermediates, supporting a proposed anaerobic degradation pathway for paracetamol. These findings underscore the potential of native sulfate reducing bacterial consortia in the bioremediation of contaminants and provide mechanistic insight into anaerobic paracetamol degradation, offering a viable strategy for enhanced treatment efficacy of contaminated waste streams.}, } @article {pmid40981149, year = {2025}, author = {Medina-Martínez, I and Gil-Gutiérrez, R and García-García, J and de la Hera-Fernández, FJ and Navarrete-Navarrete, N and Zamora-Pasadas, M and Ortego-Centeno, N and Callejas-Rubio, JL and García-García, F and Gálvez-Peralta, J and Rodríguez-Nogales, A and Correa-Rodríguez, M and Rueda-Medina, B}, title = {Association of Gut Dysbiosis with Disease Phenotype and Treatment in Systemic Lupus Erythematosus.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/medsci13030151}, pmid = {40981149}, issn = {2076-3271}, support = {20.000 €//B-CTS-100-UGR20, Consejería de Economía, Innovación y Ciencia de la Junta de Andalucía I+D+i Programa operativo FEDER Andalucía 2014-2020/ ; }, mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/drug therapy/complications ; *Dysbiosis/microbiology/complications ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; Middle Aged ; Phenotype ; Feces/microbiology ; Case-Control Studies ; }, abstract = {Introduction: Gut dysbiosis has been associated with the development of autoimmune diseases, including systemic lupus erythematosus (SLE). Although previous studies suggest microbial alterations in SLE, evidence at the species level and its clinical relevance remain limited. This study aimed to characterise the gut microbiota at species level in SLE patients and evaluate its association with clinical features. Materials and methods: A total of 57 SLE patients and 57 matched controls were included. Faecal samples were collected using the OMNIgene-GUT kit, and microbial DNA was extracted with the Maxwell RSC PureFood GMO kit. Metagenomic sequencing was performed using the Illumina MiSeq platform, and the data was analysed with QIIME2. Microbial diversity and relative abundance were assessed using the phyloseq package, and differentially abundant taxa were identified using DESeq2. Clinical subgroups among SLE patients were identified via k-means clustering. Results: SLE patients exhibited significantly different beta diversity compared to controls (p = 0.001), with increased abundance of Pseudomonadota (3.81% vs. 6.80%, p < 0.05) and decreased Bacteroidota (53.42% vs. 38.04%, p < 0.05). Only 10 bacterial species were consistently present across all SLE samples, including Akkermansia muciniphila, Bacteroides dorei, and Lactobacillus gasseri. Hypertensive patients and those treated with corticosteroids presented a marked depletion of key microbial taxa. Conversely, Belimumab-treated patients displayed a distinct microbiota enriched in species such as Alistipes shahii and Prevotella corporis. Conclusions: This study confirms significant gut microbiota alterations in SLE and pinpoints microbial profiles associated with clinical subgroups. These findings suggest gut dysbiosis may contribute to SLE pathogenesis and indicate biomarkers for disease stratification.}, } @article {pmid40977701, year = {2025}, author = {Ren, P and Zhao, Y and Li, X and Xie, J and Liao, X and Luo, Q and Liu, X and Li, J and Fan, Y and Cheng, X and Fu, X and Zhou, J and Wu, X}, title = {Comprehensive metagenomic and lipidomic analysis showed that baicalin could improve depressive behaviour in atherosclerotic mice by inhibiting nerve cell ferroptosis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1599570}, pmid = {40977701}, issn = {1664-3224}, mesh = {Animals ; *Flavonoids/pharmacology/therapeutic use ; *Ferroptosis/drug effects ; *Atherosclerosis/drug therapy/metabolism/complications ; Mice ; *Depression/drug therapy/metabolism/etiology ; *Neurons/drug effects/metabolism ; Metagenomics/methods ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Lipidomics/methods ; Disease Models, Animal ; Male ; Lipid Metabolism/drug effects ; Behavior, Animal/drug effects ; }, abstract = {BACKGROUND: Atherosclerosis (AS) concomitant depression is a serious clinical problem with unclear mechanisms of co-morbidity. Baicalin (BA) can resist atherosclerosis and depression by regulating intestinal flora and host lipid metabolism. Therefore, based on intestinal microorganisms and lipid metabolism, this study explored the mechanism of baicalin against AS concomitant depression.

METHODS: 16 C57BL/6 mice were fed with normal diet as blank control group. 48 ApoE[-/-]mice were randomly divided into 3 groups (model group and BAL, BAH two treatment groups). The mouse model of atherosclerosis concomitant depression was established by high-fat feeding combined with restraint stimulation for 16 weeks. Behavioural experiments and biochemical indexes were used to detect the antidepressant effect and anti-atherosclerosis effect of baicalin. Metagenomic sequencing technology combined with metabolomics analysis was used to detect the effects of BA on intestinal microflora structure and brain lipids in AS co-depressed mice. Erastin was used to induce HT-22 hippocampal neurons to construct a model of ferroptosis. The inhibition of baicalin on ferrotosis was verified by detecting the cell viability, ROS production, and expression levels of glutathione, SLC7A11, GPX4 and ACSL4 in each group.

RESULTS: Baicalin could effectively improve the indexes of AS co-depressed mice, and the results of metagenomics and lipidomics showed that there were disorders of intestinal flora represented by Helicobacter_typhlonius and Escherichia_coli and disorders of lipid metabolism represented by PE in the AS co-depressed model mice. The correlation analysis showed that the lipid metabolism disorders in the model mice were closely related to the intestinal flora disorders, and baicalin intervention could effectively improve the intestinal flora and lipid metabolism disorders in the AS co-depressed mice. Metabolic pathway enrichment analysis showed that differential lipid PEs were significantly enriched in the iron death pathway, and our further in vitro cellular experiments showed that baicalin could inhibit Erastin-induced Ferroptosis in the hippocampal neuronal cell line HT-22 by promoting the expression of SLC7A11, GSH, and GPX4, inhibiting the expression of ACSL4, and decreasing the cellular ROS.

CONCLUSION: Baicalin improves intestinal microbiota and brain lipid metabolism and inhibits ferroptosis of nerve cells, which possesses the application value of anti-atherosclerotic concomitant depression.}, } @article {pmid40974374, year = {2025}, author = {Hemnani, M and Karatas, M and Cruz, AVS and da Silva, PG and Thompson, G and Poeta, P and Rebelo, H and Matthijnssens, J and Mesquita, JR}, title = {Metagenomic analysis of viral diversity in Portuguese bats.}, journal = {Veterinary research communications}, volume = {49}, number = {6}, pages = {319}, pmid = {40974374}, issn = {1573-7446}, mesh = {Animals ; *Chiroptera/virology ; Metagenomics ; Portugal/epidemiology ; Feces/virology ; *Coronavirus/genetics/isolation & purification/classification ; Spike Glycoprotein, Coronavirus/metabolism/genetics ; *Coronavirus Infections/veterinary/virology/epidemiology ; Phylogeny ; }, abstract = {Bats are highly diverse mammals and known reservoirs of numerous zoonotic viruses. Their role in the ecology of emerging infectious diseases continues to be of significant interest. This study aimed to evaluate the occurrence of coronaviruses (CoVs) in Portuguese bats and predict the affinity of their spike proteins with the aminopeptidase N (APN) receptor of several host species. The study also explored the viral diversity in bat samples using metagenomic sequencing. Ten bats (five Myotis myotis and five Miniopterus schreibersii) were captured at an underground roost in 2022 (Central Portugal), and fecal samples, oral, and anal swabs were collected (n = 27). A Pan-CoV nested RT-PCR was used for initial screening, followed by viral metagenomic sequencing of all fecal samples and one CoV-positive buccal swab. In silico protein docking studies were performed between a Portuguese bat CoV spike protein and APNs of bats, pigs, and humans. Pan-CoV nested RT-PCR identified three positive samples: two fecal samples and one buccal sample. Metagenomic sequencing allowed us to determine two near complete CoV genomes. Protein docking predicted strong binding of this spike protein to bat, porcine, and human APN receptors. Metagenomics also identified picornaviruses, adenovirus, and dependoparvovirus in fecal samples. This study reports the first near complete genome sequences of two members of the Alphacoronavirus genus from a Portuguese bat The identification of other viral families highlights the diverse virome of these cave-dwelling bat species. Protein docking studies suggest a potential for cross-species transmission of this bat CoV between bats, porcines and humans, though further research is needed to confirm these interactions.}, } @article {pmid40671255, year = {2025}, author = {Bartsch, S and Kreutz, C and Scholz, KJ and Kohnert, E and Hertel, J and Wolf, M and Jakubovics, N and Al-Ahmad, A and Cieplik, F}, title = {Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity.}, journal = {Journal of dental research}, volume = {104}, number = {11}, pages = {1171-1180}, doi = {10.1177/00220345251346781}, pmid = {40671255}, issn = {1544-0591}, mesh = {*Mouth/microbiology ; Humans ; *Microbiota ; *Bacteria/classification/isolation & purification/genetics ; Archaea/isolation & purification/classification/genetics ; }, abstract = {The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence-based findings. The term "culturomics"-which describes the large-scale isolation, culture, and identification of species from an environment-was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.}, } @article {pmid40250773, year = {2025}, author = {Wu, X and Li, Y and Li, P and Lu, G and Wu, J and Wang, Z and Wen, Q and Cui, B and Wang, J and Zhang, F}, title = {Structural Variations in Ulcerative Colitis-associated Escherichia coli Reduce Fructose Utilization and Aggravate Inflammation Under High-Fructose Diet.}, journal = {Gastroenterology}, volume = {169}, number = {5}, pages = {909-924}, doi = {10.1053/j.gastro.2025.03.039}, pmid = {40250773}, issn = {1528-0012}, mesh = {*Colitis, Ulcerative/microbiology/pathology/metabolism ; *Fructose/metabolism/adverse effects ; Humans ; *Escherichia coli/genetics/metabolism/isolation & purification ; Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Mice ; Disease Models, Animal ; Adult ; Case-Control Studies ; Gene Deletion ; Middle Aged ; Escherichia coli Proteins/genetics/metabolism ; Colon/microbiology/pathology ; }, abstract = {BACKGROUND & AIMS: Structural variations (SVs) have significant effects on microbial phenotypes. The underlying mechanism of functional changes caused by gut microbial SVs in the development of ulcerative colitis (UC) need further investigation.

METHODS: We performed long-read (Oxford Nanopore Technology-based) and short-read (Illumina-based) metagenomic sequencing on stool samples from 93 patients with UC and 100 healthy controls (HCs) and analyzed microbial SVs. A total of 648 Escherichia coli (E coli) strains from fecal samples of patients with UC (UC-strains) and HCs (HC-strains) were isolated. SV-associated scrK gene deletion was verified via whole-genome sequencing or targeted polymerase chain reaction. Then, representative UC-strains, HC-strains, and scrK-knockout E coli were used for the in vitro and in vivo experiments to investigate the effects of specific SVs in E coli on fructose utilization ability and colitis.

RESULTS: E coli in UC with the highest fold change had SV-affected functional differences on fructose metabolism to that of HCs. The fructose utilization gene deletion was common in UC-strains, ostensibly reducing fructose utilization in vitro and leading to fructose-dependent aggravation of colitis in murine models. UC-strains and HC-strains induced comparable colitis under low fructose. However, high fructose exacerbated colitis severity exclusively in UC-strain-colonized mice, with elevated intestinal fructose residues, significant microbiome/metabolome changes, increased inflammation, and gut barrier disruption. These changes were mechanistically dependent on the deletion of the fructose utilization gene scrK.

CONCLUSIONS: SV-caused difference in fructose utilization and proinflammatory properties in E coli from patients with UC influence the development of UC, emphasizing the importance of fine-scale metagenomic studies in disease.}, } @article {pmid40973961, year = {2025}, author = {Lin, PT and Wu, YW}, title = {Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach.}, journal = {BMC cancer}, volume = {25}, number = {Suppl 2}, pages = {1418}, pmid = {40973961}, issn = {1471-2407}, support = {MOST110-2221-E-038-019-MY3//Ministry of Science and Technology, Taiwan/ ; MOST111-2221-E-038-023-MY3//Ministry of Science and Technology, Taiwan/ ; grant TMU-NTUST-108-08//Taipei Medical University-National Taiwan University of Science and Technology Joint Research Program/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics/diagnosis ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Asian People/genetics ; White People/genetics ; Male ; Female ; }, abstract = {BACKGROUND: Recent microbiome studies have established the association between the composition of gut microbiota and various diseases. Since 16S ribosomal RNA sequencing may suffer from problems such as lower taxonomic resolution or limited sensitivity, more and more studies embraced whole-metagenome approach, which has the potential of sequencing everything in the target microbiome, to conduct microbial association analysis. However, species profiling, which is the most popular analysis technique for whole-metagenome analysis, cannot detect uncultivated species. Since uncultivated species may also be indispensable in the gut environments, it is crucial to identify those uncultivated species and evaluate their importance in discerning disease samples from healthy ones.

RESULTS: After conducting de novo co-assembly and genome binning procedures on two colorectal cancer (CRC) cohorts, in which one of them was from the Asian population while the other was from the Caucasian population, we identified that the Asian and Caucasian cohorts shared a significant amount of microbial species in their microbiota. In addition we found that low abundance genomes may be more important in classifying disease and healthy metagenomes. By sorting the genomes based on their random forest importance scores in differentiating disease and healthy samples and cumulatively evaluating the genome subsets in predicting CRC status, we identified dozens of "important" genomes for each of the cohorts that were able to predict CRC with very high accuracy (0.90 and 0.98 AUROC for the Asian and Caucasian cohorts respectively). Uncultivated species were also identified among the selected genomes, highlighting the importance of including the uncultivated species in order to build better disease prediction models and evaluate the roles of the uncultivated species in the disease formation or progression. Finally we found that the "important" species for both cohorts did not overlap with each other, hinting that the species highly associated with CRC disease may be different between the Eastern and Western populations.

CONCLUSION: In this study we demonstrated the importance of recovering and analyzing low abundance uncultivated species to identify their associations with colorectal cancer. We hope this work shed new light on a more comprehensive understanding of how our gut microbes are correlated with diseases.}, } @article {pmid40970702, year = {2025}, author = {Hu, J and Blazier, JC and Gitter, A and Gregory, LF and Gentry, TJ}, title = {How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0172325}, doi = {10.1128/aem.01723-25}, pmid = {40970702}, issn = {1098-5336}, abstract = {UNLABELLED: River ecosystems are vital for supporting biodiversity and supplying freshwater, but are increasingly impacted by microbial pollution, including the spread of antibiotic resistance genes (ARGs), which poses growing public health concerns. While high-throughput sequencing technologies have advanced our ability to study microbial communities and resistomes, their varying capabilities and biases require comparative analysis. In this study, we compared three sequencing approaches-Illumina 16S rRNA amplicon, Illumina shotgun metagenomics, and Oxford Nanopore-based long-read metagenomics-to profile microbial communities, ARGs, and virulence factors (VFs) in 48 river water samples. All methods identified Proteobacteria and Actinobacteria as dominant phyla, but substantial differences emerged at finer taxonomic levels. Long-read metagenomics and 16S data showed greater consistency at the genus level, while Illumina metagenomics differed, detecting more potential pathogens and fewer native freshwater taxa. For ARG and VF profiling, unassembled Illumina data yielded higher diversity and abundance, but assembled Illumina data showed comparable results to long-read metagenomics data in terms of dominant genes and host associations. Although Illumina provides high sensitivity, the use of short reads and associated assembly limitations can compromise functional accuracy. In contrast, long-read metagenomics facilitates gene-level resolution and direct host linkage, providing a more comprehensive understanding of environmental microbiomes. Our findings highlight the strengths and limitations of each method and support Oxford Nanopore technology (ONT)-based long-read metagenomic sequencing as a cost-effective and informative tool for high-resolution taxonomic and functional analysis of complex environmental samples.

IMPORTANCE: Accurate characterization of microbial communities and their functional traits, such as antibiotic resistance, is essential for evaluating water quality and associated public health risks. However, the selection of sequencing methods can substantially influence the detection and interpretation of microbial community composition and functional potential in environmental samples. By directly comparing amplicon, short-read metagenomic, and long-read metagenomic sequencing across 48 freshwater samples collected across different sites and time points, this study builds upon earlier work that typically focused on only two methods or less complex communities. It provides a comparative evaluation of three widely used sequencing approaches, demonstrating how methodological differences affect the resolution and reliability of taxonomic and functional profiling in complex environmental microbiomes. By highlighting the strengths and limitations of each platform, these findings enhance our understanding of how sequencing strategy shapes environmental microbiome analyses and contributes to evidence-based method selection in environmental microbiology and antimicrobial resistance monitoring.}, } @article {pmid40961652, year = {2025}, author = {Gao, X and Ning, P and Luo, S and Wang, Y and Li, W and Fan, X and Li, X}, title = {Microbiome and pathogen identification, and associated antimicrobial resistance genes and virulence factors in seafood revealed by 16S rRNA amplicon and metagenomic sequencing.}, journal = {International journal of food microbiology}, volume = {443}, number = {}, pages = {111441}, doi = {10.1016/j.ijfoodmicro.2025.111441}, pmid = {40961652}, issn = {1879-3460}, mesh = {*Seafood/microbiology ; *Virulence Factors/genetics ; *Bacteria/genetics/isolation & purification/drug effects/classification/pathogenicity ; Animals ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Fishes/microbiology ; *Microbiota ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology ; Shellfish/microbiology ; }, abstract = {16S rRNA amplicon sequencing and metagenomic next-generation sequencing (mNGS) were employed to comprehensively analyze the microbial communities, foodborne pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in four seafood categories: ready-to-eat fish (RET-fish), non-ready-to-eat fish (non-RTE-fish), shellfish, and shrimp. At the phylum level, Pseudomonadota dominated across all samples. The microbial community composition of shellfish exhibited significant distinctions compared to other seafood categories. Metagenomic profiling identified high-risk pathogens, such as pathogenic Vibrio, Salmonella enterica, and Listeria monocytogenes. ARGs and VFs displayed the highest relative abundance in RET-fish, while shellfish exhibited the lowest abundance with statistically significant differences compared to other groups. For ARGs carried hosts, Bacillus-associated tet(L) and Lactobacillus-associated Inu(A) in RTE-fish demonstrated elevated abundance. In contrast, Vibrio species in other groups carried high abundances of ARGs such as qnrS and tet(34). Additionally, Vibrio harbored high levels of VFs, such as flagella and EF-Tu. Furthermore, plasmid-derived contigs co-harboring ARGs and mobile genetic elements (MGEs) were identified, displaying broad host ranges and high homology with plasmids from previously isolated clinical pathogenic strains, which underscores the potential role of seafood as a critical reservoir for the dissemination of ARGs. High-throughput sequencing approaches, integrated with multi-tool bioinformatics pipelines, provided robust insights into microbial communities and associated safety risk factors. These findings highlight the urgent need for targeted surveillance of seafood products and stricter antibiotic regulations in aquaculture to mitigate public health risks posed by foodborne pathogens and antimicrobial resistance.}, } @article {pmid40834509, year = {2025}, author = {Poshvina, DV and Balkin, AS and Dilbaryan, DS and Vasilchenko, AS}, title = {Unravelling the response of the soil microbiome to macrolactin A: A metagenomic study.}, journal = {Chemosphere}, volume = {387}, number = {}, pages = {144645}, doi = {10.1016/j.chemosphere.2025.144645}, pmid = {40834509}, issn = {1879-1298}, mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Macrolides/pharmacology ; Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Rhizosphere ; Soil/chemistry ; }, abstract = {The development of environmentally sustainable biopreparations for crop protection requires comprehensive assessment of their microbiome impacts. This study investigates how macrolactin A (McA)-a polyketide antibiotic produced by plant-beneficial Bacillus velezensis-shapes soil microbial communities and antibiotic resistance gene (ARG) profiles under various agricultural scenarios. Using high-throughput metagenomics and network analysis, we compared untreated soils with those exposed to two McA concentrations: a high dose (10 mg/kg soil, representing potential point-source accumulation) and a low dose (1 mg/kg, mimicking natural rhizosphere levels). While overall ARG α- and β-diversity remained stable, we observed significant taxonomic restructuring, with Pseudomonadota increasing by 1.36-2.15 % and Actinomycetota declining by 1.14-1.74 % across treatments. Resistome analysis showed dose-dependent ARG selection: control soils favored target alteration mechanism, whereas McA promoted efflux, inactivation, and protection mechanisms. Network analysis demonstrated disruption of complex ARG-host associations, as control-dominant genera belonging to Actinomycetota (Conexibacter, Baekduia, and Capillimicrobium) maintaining 16-21 ARGs per genome decreased, while genera belonging to Pseudomonadota (Bradyrhizobium, Mesorhizobium, Paraburkholderia, and Piscinibacter) with streamlined resistomes (1-2 ARGs) became prevalent. Functional gene profiling (COGs) and annotation of MAGs revealed dose-dependent restructuring: low-dose McA enriched chemotaxis systems and broad-spectrum efflux pumps, facilitating motile escape and energy-efficient resistance, whereas high-dose exposure selected for secondary metabolite synthesis, metal transporters, and cell wall remodeling genes, indicating defensive countermeasures. These findings demonstrate McA's biphasic selection: low doses favor avoidance strategies (efflux/motility), while high doses enforce biosynthetic defenses and structural resilience. The results support the hypothesis that narrow-spectrum antibiotics act as ecosystem engineers through metabolic trade-offs, highlighting the need to evaluate resistome restructuring in biocontrol agent risk assessments.}, } @article {pmid40970218, year = {2024}, author = {Finn, RD and Balech, B and Burgin, J and Chua, P and Corre, E and Cox, CJ and Donati, C and Dos Santos, VM and Fosso, B and Hancock, J and Heil, KF and Ishaque, N and Kale, V and Kunath, BJ and Médigue, C and Nogueira, T and Pafilis, E and Pesole, G and Richardson, L and Santamaria, M and Strepis, N and Van Den Bossche, T and Vizcaíno, JA and Zafeiropoulos, H and Willassen, NP and Pelletier, E and Batut, B}, title = {Establishing the ELIXIR Microbiome Community.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {}, doi = {10.12688/f1000research.144515.2}, pmid = {40970218}, issn = {2046-1402}, mesh = {*Microbiota ; *Metagenomics/methods ; Computational Biology ; }, abstract = {Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.}, } @article {pmid40969555, year = {2025}, author = {Zhang, Y and Zhang, Y and Xing, G and Mei, T and Wang, M and Huang, C and Yi, H and Zhan, Y and Yang, S and Yan, Q and Li, S and Chen, C}, title = {Characterization of the oral virome in patients with diabetes mellitus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1607798}, pmid = {40969555}, issn = {2235-2988}, mesh = {Humans ; *Virome ; *Mouth/virology/microbiology ; Male ; Female ; *Diabetes Mellitus/virology/microbiology ; Middle Aged ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Microbiota ; Bacteria/classification/genetics ; Adult ; Aged ; Dysbiosis ; Metagenome ; }, abstract = {INTRODUCTION: Diabetes mellitus (DM), a globally prevalent chronic metabolic disorder characterized by persistent hyperglycemia, has been increasingly linked to dysbiosis of the oral microbiome. However, the relationship between the virome, a crucial component of the oral microbiome, and DM remains poorly understood.

METHODS: To explore the characteristics of the oral virome in DM patients, we analyze the oral viral communities of 45 DM patients and 40 healthy controls (HC) using a publicly available metagenomic dataset.

RESULTS: Our analysis revealed no significant differences in a-diversity between DM patients and HC. However, Podovirus was enriched in DM patients, whereas Microviridae was more prevalent in HC. A total of 1,131 virus signal was identified, primarily belonging to the Siphovirus and Myovirus taxa. Notably, HC-enriched vOTUs exhibited broader host tropism, predominantly infecting Prevotella, Fusobacterium, and Gemella, whereas DM-enriched vOTUs showed narrower specificity for Pauljensenia and Veillonella. Cross-kingdom network analysis suggested that certain viruses (HMP_1157.k81_309051) may have potential links to the development of DM, and the bacteria genus F0040 might play a significant role in maintaining oral health. Additionally, the random forest model based on viral markers effectively distinguished between HC and DM patients (AUC =90.8%), significantly outperforming the bacterial model.

DISCUSSION: This indicates that these unique viral markers could serve as potential targets for DM intervention. Taken together, our findings reveal distinct alterations in the oral virome of DM patients and highlight its promise as a novel diagnostic and therapeutic target in metabolic disease research.}, } @article {pmid40969552, year = {2025}, author = {Wang, J and Ren, W and Liu, S and Li, Z and Zeng, Y and Meng, J and Yao, X}, title = {Changes in antioxidant capacity and gut microbiota in mice after intake of camel milk.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1621031}, pmid = {40969552}, issn = {2235-2988}, mesh = {Animals ; Camelus ; *Gastrointestinal Microbiome ; *Antioxidants/metabolism/analysis ; *Milk/chemistry ; Mice ; Mice, Inbred ICR ; Liver/metabolism ; Bacteria/classification/genetics/isolation & purification ; Colon/microbiology ; Metagenomics ; Male ; Fermentation ; Probiotics/administration & dosage ; }, abstract = {Fermented camel milk offers significant nutritional benefits, enriched with probiotics that generate bioactive compounds advantageous to human health. In order to investigate the effects of camel milk with different treatments on Antioxidant Capacity and Gut Microbiota in mice, 32 ICR mice were selected and randomly divided into 4 groups, including gavage with 10 mL/kg body weight of distilled water (DW Group), camel milk (CM Group), fermented camel milk (FCM Group), and pasteurized fermented camel milk (PFCM Group) every morning, respectively. After 28 days, liver and colon samples were collected to assess liver antioxidant capacity, and metagenomic analysis was performed on alterations in microbial community structures. Results demonstrated that all camel milk treatments elevated liver total protein levels while reducing MDA and SOD activity. In addition, the PFCM group had the highest total antioxidant capacity and the lowest SOD content. In addition, the intestinal microorganisms of mice changed at the phylum, genus and species levels after being gavaged with camel milk of different treatments. A total of 4732 microorganisms were identified, of which 259, 222, 116 and 164 were unique to the DW, CM, FCM and PFCM groups, respectively. The relative abundances of Adlercreutzia caecimuris, Adlercreutzia mucosicola and Enterorhabdus sp. P55 were significantly higher in the CM, FCM and PFCM groups than in the DW group, and the relative abundances of Parvibacter caecicola, Adlercreutzia muris and Roseburia sp. 1XD42-69 were significantly higher in the CM and PFCM groups than in the DW group. In addition, the relative abundances of Faecalibaculum rodentium, Alistipes muris and Limosilactobacillus reuteri were different between the CM and FCM groups. The results of the correlation analysis between the relative abundance of microbial species and antioxidant indices showed that Adlercreutzia mucosicola, Adlercreutzia muris, Lactobacillus acidophilus, and Enterorhabdus sp. P55 were significantly correlated with the antioxidant indices of mice. Further functional annotations indicated that these microorganisms might modulate antioxidant activity via metabolic and organismal systems. In summary, camel milk and fermented camel milk can play a positive role in regulating the intestinal flora of mice, thereby regulating the antioxidant capacity of mice and alleviating the effects of oxidative stress on the body. This study provides a scientific foundation for the further exploration and utilization of camel milk.}, } @article {pmid40968405, year = {2025}, author = {Trubl, G and Probst, AJ}, title = {Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70177}, doi = {10.1111/1462-2920.70177}, pmid = {40968405}, issn = {1462-2920}, support = {SCW1632//U.S. Department of Energy Office of Biological and Environmental Research through the Genomic Science Program and the Lawrence Livermore National Laboratory/ ; CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; 426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Terminology as Topic ; *Ecology ; *Microbiota ; *Microbiology ; Communication ; }, abstract = {The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.}, } @article {pmid40967861, year = {2025}, author = {Ma, Y and Si, JH and Sun, DJY and Yu, CQ and Pang, YJ and Lyu, J and Li, LM}, title = {[Progress in population-based research of human microbiome and cardiovascular diseases].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {46}, number = {9}, pages = {1680-1687}, doi = {10.3760/cma.j.cn112338-20241219-00816}, pmid = {40967861}, issn = {0254-6450}, support = {2023ZD0510101, 2023ZD0510100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, mesh = {Humans ; *Cardiovascular Diseases/microbiology ; *Microbiota ; Metagenomics ; }, abstract = {The human microbiome encompasses a diverse array of microorganisms and their functional interactions within the human body. It exhibits a vast diversity of species and complex roles across various body environments. Advanced sequencing technologies, such as 16S amplicon sequencing and metagenomic sequencing, facilitate in-depth analysis on this microbial community. Recent researches have suggested that characteristics of the human microbiome (such as diversity and composition of microbiome, involving metabolic pathways and metabolites) might be associated with the onset and progression of cardiovascular diseases. These findings provide valuable insights into the etiology of chronic diseases and might aid in the development of novel disease biomarkers and intervention strategies. This paper summarizes the designs, current status and key findings of current population-based research in this field, and introduce the future development and analyze the existing critical problems that need further investigations.}, } @article {pmid40835198, year = {2025}, author = {Liu, Q and Wang, M and Xie, JW and Du, YT and Yin, ZG and Cai, JH and Zhao, MH and Jiang, YT and Zhang, HD}, title = {Macrogenome analysis of rodents from Heilongjiang Province, China.}, journal = {Acta tropica}, volume = {270}, number = {}, pages = {107789}, doi = {10.1016/j.actatropica.2025.107789}, pmid = {40835198}, issn = {1873-6254}, mesh = {Animals ; China ; *Viruses/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; *Rodentia/microbiology/virology ; *Murinae/microbiology/virology ; *Arvicolinae/microbiology/virology ; *Microbiota ; Phylogeny ; *Metagenome ; Disease Reservoirs/virology/microbiology ; Zoonoses ; }, abstract = {Rodents are carriers and hosts of numerous zoonotic pathogens, analysing the diversity of viruses and bacteria carried by rodents is important for predicting and reducing the risk of future outbreaks of zoonotic diseases. Heilongjiang is a border province in China with rich ecological resources. In this study, we characterized the zoonotic microbiota (viruses and bacteria) in wild rodents. Sixty-seven rodents representing two species (20 Apodemus peninsulae; 47 Myodes rufocanus) were collected in Hengdaohezi Town, Heilongjiang Province, China. Metagenomic sequencing was employed to characterize pathogen carriage in these reservoirs. The sequencing results showed that the annotated viruses covered 21 viral families, including family Arenaviridae and family Hantaviridae. The annotated bacteria cover 1051 bacterial genera, including genus Salmonella and genus Yersinia. Results of de novo assembly of extracted viral sequences using Megahit showed that 154 contigs were assembled from these two hosts, and 110 of these contigs were mapped to 19 viruses from eight families, including Rat arterivirus1, Amur virus and Lassa mammarenavirus, these results can provide a certain reference for the monitoring and control of rodents in Heilongjiang Province.}, } @article {pmid40744013, year = {2025}, author = {Arnoldini, M and Sharma, R and Moresi, C and Chure, G and Chabbey, J and Slack, E and Cremer, J}, title = {Quantifying the varying harvest of fermentation products from the human gut microbiota.}, journal = {Cell}, volume = {188}, number = {19}, pages = {5332-5342.e16}, doi = {10.1016/j.cell.2025.07.005}, pmid = {40744013}, issn = {1097-4172}, support = {R01 GM149611/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Fermentation ; Bacteria/metabolism/genetics ; Dietary Carbohydrates/metabolism ; Metagenomics ; Diet ; Mucins/metabolism ; }, abstract = {Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2%-5% of human energy demand for Western diets and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.}, } @article {pmid40048707, year = {2025}, author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A}, title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: An ancillary study from the BLOCAGE trial.}, journal = {Neuro-oncology}, volume = {27}, number = {8}, pages = {2090-2104}, doi = {10.1093/neuonc/noaf059}, pmid = {40048707}, issn = {1523-5866}, support = {INCa-DGOS-Inserm_12560//SiRIC CURAMUS/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Central Nervous System Neoplasms/drug therapy/microbiology/pathology/mortality ; Male ; Female ; Middle Aged ; Prospective Studies ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; Methotrexate/administration & dosage/therapeutic use ; Prognosis ; *Lymphoma/drug therapy/microbiology/pathology ; Survival Rate ; Follow-Up Studies ; Adult ; }, abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate-based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.

METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first-line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n = 52), cerebrospinal fluid (CSF, n = 52), and plasma samples (n = 35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.

RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine-valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine-valine content confirmed these clinical associations.

CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.}, } @article {pmid40965271, year = {2025}, author = {Dell'Acqua, AN and Scicchitano, D and Simoncini, N and Mercanti, I and Leuzzi, D and Turroni, S and Corlatti, L and Rampelli, S and Colonna, M and Corinaldesi, C and Candela, M and Palladino, G}, title = {Ski Tourism Shapes the Snow Microbiome on Ski Slopes in the Italian Central Alps.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70195}, doi = {10.1111/1758-2229.70195}, pmid = {40965271}, issn = {1758-2229}, mesh = {Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Skiing ; *Snow/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Tourism ; Humans ; Viruses/classification/genetics/isolation & purification ; Metagenomics ; Seasons ; }, abstract = {Winter sports exert significant anthropogenic pressures on the snow microbiome, affecting the entire alpine ecosystem. The massive usage of artificial snow, human occupation, and the release of xenobiotics like microplastics or ski wax components on ski tracks can profoundly alter snow microbial ecology. Here, we reconstructed the temporal dynamics of the snow microbiome at three sites in the Italian Alps: inside and outside a ski track at the impacted site of Santa Caterina Valfurva and near Cancano lake as an unimpacted control. Using epifluorescence microscopy, 16S rRNA amplicon sequencing, and inferred metagenomics, we found that the snow microbiome inside the track presented a higher load of prokaryotes and viruses. Notably, N2-fixing microorganisms from cryospheric environments and host-associated taxa, like Terrisporobacter, Clostridium sensu stricto, Enterococcus, and Muribaculaceae, and the opportunistic pathogen Citrobacter characterised the impacted site. These microorganisms could originate from the river water used to produce artificial snow during winter. Our findings highlight the complexity and multifunctionality of the snow microbiome, where microorganisms with different ecological propensities can coexist, and the detectable impact of ski tourism, which enriches host-associated and xenobiotic-degrading microorganisms. This underscores the need for systematic monitoring and protection of the snow microbiome in the Alpine environment from anthropogenic threats.}, } @article {pmid40964625, year = {2025}, author = {López Clinton, S and Iwaszkiewicz-Eggebrecht, E and Miraldo, A and Goodsell, R and Webster, MT and Ronquist, F and van der Valk, T}, title = {Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.}, journal = {Ecology and evolution}, volume = {15}, number = {9}, pages = {e72163}, pmid = {40964625}, issn = {2045-7758}, abstract = {Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.}, } @article {pmid40963595, year = {2025}, author = {Wang, Q and Luo, Y and Mao, C and Xiang, X and Chen, J}, title = {Combined metagenomic and metabolomic analyses reveal gut microbiota dysbiosis and metabolic dysfunction in pediatric neurodevelopmental disorders.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1645137}, pmid = {40963595}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Metabolomics/methods ; *Metagenomics/methods ; Child, Preschool ; *Dysbiosis/metabolism/microbiology ; *Neurodevelopmental Disorders/metabolism/microbiology/etiology ; Child ; Feces/microbiology ; Metabolome ; }, abstract = {INTRODUCTION: Neurodevelopmental disorders (NDDs) are chronic brain diseases linked to innate immune signaling abnormalities, affecting children with complex gut-brain axis etiologies and limited targeted therapies. While infant microbes/metabolites may predict childhood NDDs, their landscape and host-metabolism interactions in NDDchildren remain unclear.

METHODS: This study enrolled 40 NDDchildren (mean age: 5.18 ± 1.77, F:M = 11:29) and 60 healthy controls (HCs; mean age:5.11 ± 1.42, F:M = 25:35) from Gansu Province Hospital Rehabilitation Center. Shotgun metagenomics and untargeted metabolomics was used to analyze gut microbiota and fecal/plasma metabolites, multi-omics integration analysis was performed to explore host-microbe interactions.

RESULTS: Clinically, NDD children showed self-care, concentration, and social behavior deficits, with grandparents as primary caregivers, versus parents in HCs. Microbiome analysis revealed reduced gut diversity and dysregulation in NDDs: depleted beneficial taxa including Akkermansia muciniphila and Lactococcus lactis, but enriched GABA/lactateproducing bacteria; and disrupted pathways included polysaccharides/fatty acids/amino acid/purine ribonucleosides metabolism. Fecal metabolomics identified 100 enriched metabolites including polyamines and GABA in 45 pathways and 254 depleted metabolites including bile acids and butyrate in 57 pathways. Plasma metabolomics showed 321 enriched metabolites like free fatty acids in 143 pathways and 270 depleted metabolites including glycerophospholipids in 84 pathways. Notably, phenolic acids, arginine/proline metabolism, and HIF-1 signaling were enriched in both feces and plasma of NDDs children. Benzene derivatives, indoles, steroid hormone biosynthesis, and tryptophan/tyrosine/phenylalanine metabolism were increased in plasma but decreased in feces, while oxidized lipids, amino acids and derivatives, metabolism of glycine/serine/threonine, alanine/aspartate/glutamate, and cysteine/methionine showed the opposite pattern. Venn analysis identified 29 common metabolites, with eight in KEGG maps. 11-dehydrocorticosterone, LPC (17:0/0:0), adipic acid, and sucralose were decreased in feces but increased in plasma; 1-methylhistidine and trigonelline were decreased in both; L-asparagine anhydrous was increased in feces but decreased in plasma; and sarcosine increased in both. Microbe-metabolite correlation analyses linked these metabolites to NDDs depleted species A. muciniphila, L. lactis, A. butyriciproducens, and etc.

DISCUSSIONS: Collectively, our study presents the first integrated profile of gut microbiome, microbial metabolites, and host metabolome, reveals gut microbiota dysbiosis, functional impairment, and metabolic disturbance in pediatric NDDs. These findings provide a theoretical foundation for microbiotaand metabolite-targeted therapeutic strategies in childhood NDDs.}, } @article {pmid40958540, year = {2025}, author = {Wang, X and Wang, W and Deng, L and Li, T and Lei, S and Zhang, L and Liao, L and Song, Z and Liu, G and Zhang, C}, title = {Shifts in Genome Size and Energy Utilization Strategies Sustain Microbial Functions Along an Aridity Gradient.}, journal = {Global change biology}, volume = {31}, number = {9}, pages = {e70498}, doi = {10.1111/gcb.70498}, pmid = {40958540}, issn = {1365-2486}, support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Genome Size ; Desert Climate ; *Energy Metabolism ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbes acquire energy to sustain their survival and function through the decomposition of organic carbon (C) or by oxidizing atmospheric trace gases (e.g., H2, CO, CH4). However, how these two microbial energy-acquisition strategies change along environmental gradients and the underlying mechanisms are unclear. This study investigated the energy strategies and genomic traits of soil microbiomes along a natural aridity gradient, ranging from semi-humid forests to arid deserts. By analyzing 374 metagenome-assembled genomes from 13 microbial phyla, we found that the most prevalent microbes are metabolically versatile aerobes that use atmospheric trace gases to support aerobic respiration, C fixation, and N, P, and S cycling. Soil microbes adapt genomic traits associated with reduced energy expenditure in more arid soils, including smaller genome sizes, lower GC content, and fewer 16S rRNA gene copies. Microbial communities in diverse arid habitats are capable of utilizing organic compounds and the oxidation of trace gases (e.g., H2, CO, CH4, and H2S) as energy sources. However, the utilization of organic energy decreased while reliance on trace gas oxidation increased with increasing aridity. Higher consumption rates of H2, CO, and CH4 in desert soils from ex situ culture experiments confirmed that increased aridity stimulates microbial oxidation of atmospheric trace gases. This shift in energy utilization was strongly correlated with declining soil organic C levels. As organic C decreased along the aridity gradient, the abundance of trace gas oxidizers (both specialized and multi-gas oxidizers) increased significantly, while that of non-oxidizers declined. Trace gas oxidizers exhibited smaller genomes, lower 16S rRNA operon copy numbers, and slower predicted growth rates, indicative of oligotrophic lifestyles. In contrast, copiotrophic non-oxidizers had larger genomes and faster growth rates. These findings reveal that microbial communities adapt their genomic traits and energy-acquisition strategies to sustain functionality across aridity gradients, enhancing our understanding of soil microbiome responses to climate change.}, } @article {pmid40849730, year = {2025}, author = {Zhou, SY and Lie, Z and Lei, C and Zhang, Q and Liu, X and Wu, G and Neilson, R and Huang, FY and Chu, G and Meng, Z and Zhu, D and Tissue, DT and Peñuelas, J and Liu, J}, title = {Multi-scale evidence for declining microbial carbon fixation along forest succession gradients.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf191}, pmid = {40849730}, issn = {1751-7370}, support = {42477132//National Natural Science Foundation of China/ ; 42207158//National Natural Science Foundation of China/ ; 32101342//National Natural Science Foundation of China/ ; 2022B1111230001//Key-Area Research and Development Program of Guangdong Province/ ; 2024B1212080005//Science and Technology Program of Guangdong/ ; 2024B1212070012//Science and Technology Program of Guangdong/ ; TED2021-132627//Spanish Government/ ; B-I00//Spanish Government/ ; PID2022-140808NB-I00//Spanish Government/ ; AEI/10.13039/501100011033//Spanish Government/ ; SGR 2021-1333//European Union Next Generation EU/PRTR/ ; }, mesh = {*Forests ; *Soil Microbiology ; *Carbon Cycle ; *Bacteria/metabolism/classification/genetics ; *Fungi/metabolism/classification/genetics ; Carbon/metabolism ; Metagenomics ; Carbon Dioxide/metabolism ; Microbiota ; Isotope Labeling ; Carbon Isotopes/metabolism ; Soil/chemistry ; }, abstract = {Although soil carbon accumulates during subtropical forest succession, changes in microbial communities and their carbon fixation capacity remain unclear. Using an integrative approach that combines field experimentation, extensive global metagenomic data, and isotope labelling, we analysed 84 soil microbiomes from a long-term successional site and 755 global metagenomes to investigate microbial community dynamics and their role in carbon fixation. Based on field data, bacteria, fungi, and protists had synchronous succession with vegetation; however, the relative abundance of carbon fixation genes declined significantly in later successional stages. To further investigate this outcome, we analysed global data from planted and mature natural forests and found significantly higher carbon fixation potential in planted forests, predominantly driven by Pseudomonadota and Actinomycota members. Field-based 13C labelling results further confirmed a significant decline in microbial CO2 fixation rates with forest succession. These findings underscore the ecological importance of microbial carbon fixation in early forest succession, emphasizing its foundational role in initiating soil carbon accumulation and shaping long-term carbon cycling trajectories.}, } @article {pmid40795332, year = {2025}, author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW}, title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf171}, pmid = {40795332}, issn = {1751-7370}, mesh = {Anaerobiosis ; *Microbiota ; Hydrogen/metabolism ; *Bacteria/metabolism/classification/genetics ; *Eukaryota/growth & development ; Metagenomics ; Symbiosis ; }, abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.}, } @article {pmid40752853, year = {2025}, author = {Santiwijai, M and Taoka, Y}, title = {Effect of Bacillus subtilis and fungal enzymes on immune responses and gut microbiota of masu salmon (Oncorhynchus masou masou).}, journal = {Developmental and comparative immunology}, volume = {170}, number = {}, pages = {105424}, doi = {10.1016/j.dci.2025.105424}, pmid = {40752853}, issn = {1879-0089}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Bacillus subtilis/immunology ; *Probiotics/administration & dosage ; Muramidase/blood/metabolism ; *Salmon/immunology/microbiology ; *Aspergillus ; Fish Proteins/metabolism/genetics ; }, abstract = {The effects of oral administration of probiotics Bacillus subtilis (BS) and Aspergillus sojae-fermented materials (AFM) supplementation on immune responses and the gut microbiome of masu salmon Oncorhynchus masou masou were evaluated. Masu salmon (44.07 ± 7.1 g) were individually raised on a commercial diet without supplementation (control group), with B. subtilis strain DB9011 at 1.0 × 10[6] cfu/g-feed (BS group), and with A. sojae-fermented materials supplementation at 0.2 % (AFM group) for 24 days. Lysozyme activity in fish serum was determined using turbidimetric assays. Immune-related gene expression and gut microbiota were analyzed through real-time PCR and metagenomics analysis with a next-generation sequencer, respectively. Both the BS and AFM groups showed higher lysozyme activity but lower serum protein concentrations compared to the control group without significant different. The gut bacterial composition in the BS and AFM groups was dramatically different compared to that in the control group. The alpha diversity of the BS group showed significantly greater richness in terms of Chao1, faith_pb, and shannon_entropy. Conversely, the alpha diversity of the AFM group showed significantly greater richness only on faith_pb. The expression of immune-related genes such as TNF-α and IFN-γ was upregulated in the treatment group compared to the control group. IL1-β was upregulated in the AFM group. Regarding IL1-β, no differences were observed between the control and BS group. Thus, results indicated that oral administration of the BS and AFM modify gut microbiota and stimulated the expression of immune-gene expression.}, } @article {pmid40958166, year = {2025}, author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG}, title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70178}, doi = {10.1111/1462-2920.70178}, pmid = {40958166}, issn = {1462-2920}, support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; }, abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.}, } @article {pmid40953197, year = {2025}, author = {Ogarkov, O and Orlova, E and Suzdalnitsky, A and Mokrousov, I}, title = {Microbiota of the Lung Tuberculoma: Paucibacillary Bacterial Community.}, journal = {International journal of mycobacteriology}, volume = {14}, number = {3}, pages = {209-218}, pmid = {40953197}, issn = {2212-554X}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Mycobacterium tuberculosis/genetics/isolation & purification/classification ; *Microbiota ; *Tuberculoma/microbiology ; *Lung/microbiology/pathology ; *Tuberculosis, Pulmonary/microbiology ; }, abstract = {Caseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-resistant persisting Mycobacterium tuberculosis (MTB). However, tubercle bacilli are not the only bacterial inhabitants of this necrosis. We discuss the available data on metagenomic and amplicon sequencing of 16S rRNA of caseous necrosis from surgically excised tuberculosis (TB) foci. This approach facilitated the characterization of the biodiversity and the potential biochemical pathways of these bacterial communities. We postulate that in terms of MTB content relative to satellite anaerobic lipophilic bacteria, caseum may present two distinct terminal states. "True" TB necrosis, containing 99.9% tubercle bacilli, and a polymicrobial community wherein anaerobic lipophilic bacteria predominate over MTB. Isolation from caseum and genomic characterization of several Corynebacterium and Staphylococcus species support this concept.}, } @article {pmid40914165, year = {2025}, author = {Anani, H and Destras, G and Bulteau, S and Castain, L and Semanas, Q and Burfin, G and Petrier, M and Martin, FP and Poulain, C and Dickson, RP and Bressollette-Bodin, C and Roquilly, A and Josset, L}, title = {Lung virome convergence precedes hospital-acquired pneumonia in intubated critically ill patients.}, journal = {Cell reports. Medicine}, volume = {6}, number = {9}, pages = {102289}, doi = {10.1016/j.xcrm.2025.102289}, pmid = {40914165}, issn = {2666-3791}, mesh = {Humans ; *Virome ; Critical Illness ; *Lung/virology/microbiology ; Male ; Female ; Middle Aged ; *Healthcare-Associated Pneumonia/virology/microbiology ; Aged ; Microbiota ; Bacteriophages ; Dysbiosis/microbiology ; *Cross Infection/microbiology/virology ; Streptococcus/virology ; Intubation, Intratracheal ; }, abstract = {Hospital-acquired pneumonia (HAP) is one of the most common nosocomial infections, leading to significant morbidity and mortality in critically ill patients. HAP is previously associated with dysbiosis of the microbiota. However, the composition of the lung virome and its role in HAP pathogenesis remain unclear. Here, we longitudinally analyze the endotracheal virome in 87 critically ill patients, including 48 with HAP. Within the virome dominated by Caudoviricetes, a decrease in viral beta-diversity toward a bacteriophage-dominated signature and a distinct viral-bacterial interactome is observed 5-4 days before HAP onset. Lung virome composition, viral convergence before HAP onset, and conservation of 18% of the bacteriophage signature are validated in an external cohort of 40 patients. In silico causal inference further identifies bacteriophages associated with Streptococcus and Prevotella as a key regulator of HAP onset. These findings suggest an uncovered pathophysiological mechanism of HAP with virome involvement in lung microbiota dysbiosis. The discovery and validation studies are registered at ClinicalTrials.gov (NCT02003196 and NCT04793568).}, } @article {pmid40897178, year = {2025}, author = {Xu, T and Jiao, X and Liu, G and Chen, X and Luo, Q and Zhang, G and Li, B and Zhang, Y and Li, X and Cheung, Y and Chai, X and Huang, Y and Wu, H and Deng, F and Chen, F and Liang, G}, title = {Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes.}, journal = {Cell reports. Medicine}, volume = {6}, number = {9}, pages = {102325}, doi = {10.1016/j.xcrm.2025.102325}, pmid = {40897178}, issn = {2666-3791}, mesh = {Humans ; *Porphyromonas gingivalis/virology ; *Diabetes Mellitus, Type 2/microbiology/virology ; *Virome/genetics ; *Bacteriophages/genetics ; *Obesity/microbiology/virology ; *Mouth/virology/microbiology ; *Metagenomics/methods ; *Metagenome ; Female ; Male ; Middle Aged ; Gastrointestinal Microbiome ; Microbiota ; }, abstract = {The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a freely accessible online resource cataloging 24,440 bacteriophage viral operational taxonomic units and 83 eukaryotic viral genomes. Utilizing HOVD, we investigate oral virome variation and its correlation with oral bacteria and gut virome in 220 obese individuals with or without type 2 diabetes mellitus (T2D). Obese individuals with T2D exhibit reduced oral viral diversity, lower correlations with clinical features, disrupted viral-bacterial correlations, and enhanced oral-gut virome transmission. Furthermore, we computationally identify bacteriophages that infect Porphyromonas gingivalis and screen six putative endolysins. Experimental validation reveals that a mixture of three endolysins significantly inhibits Porphyromonas gingivalis growth. These findings highlight the potential of phage-derived endolysins for periodontitis with T2D, offering a path toward oral and systemic disease intervention.}, } @article {pmid40848515, year = {2025}, author = {Ni, J and Fu, L and Xiao, J and Li, C and Wu, X and Yuan, Z and Wang, J and Tang, S and Deng, F and Shen, S}, title = {Metagenomic evidence of viral secretion from tick salivary glands to saliva: implications for potential horizontal transmission.}, journal = {Ticks and tick-borne diseases}, volume = {16}, number = {5}, pages = {102540}, doi = {10.1016/j.ttbdis.2025.102540}, pmid = {40848515}, issn = {1877-9603}, mesh = {Animals ; *Saliva/virology ; Salivary Glands/virology ; *Ixodidae/virology ; China ; *Viruses/genetics/isolation & purification/classification ; *Virome ; Metagenomics ; Female ; *Metagenome ; }, abstract = {Ticks transmit diverse viral pathogens to hosts during blood-feeding via saliva secretion. This study characterized viral compositions in salivary glands and saliva from adults of four tick species (Ixodes persulcatus, Rhipicephalus microplus, Haemaphysalis longicornis, and Haemaphysalis concinna) collected in China. Meta-transcriptomic analysis revealed distinct viromes across species, with Flaviviridae dominant in R. microplus, Nairoviridae in H. concinna and I. persulcatus, and Phenuiviridae in H. longicornis and I. persulcatus. Among 27 viruses detected in salivary glands, 14 were identified in saliva, indicating horizontal transmission potential. Viruses with higher abundance (transcripts per thousand bases per million, TPM) in salivary glands were more likely to be secreted in saliva. Genomic sequences of eight viruses, including severe fever with thrombocytopenia syndrome virus (SFTSV), tick-borne encephalitis virus (TBEV), Jingmen tick virus (JMTV), Songling virus (SGLV), Wetland virus (WELV), Beiji nairovirus (BJNV), Mukawa virus (MKWV), and Wuhan tick virus 2 (WHTV2), which are associated with human diseases or possess spillover potentials, were fully assembled from salivary glands and confirmed in saliva. Notably, SFTSV in H. longicornis; MKWV, Sichuan tick hepe-like virus, and Jilin luteo-like virus 2 in I. persulcatus; and JMTV in R. microplus showed significantly increased abundance in saliva, indicating an enhanced secretion of these viruses into saliva. Conversely, TBEV, BJNV, and Sara tick phlebovirus in I. persulcatus, SGLV and WELV in H. concinna, and WHTV2 in R. microplus exhibited reduced salivary abundance despite glandular presence. These findings demonstrate differential secretion capabilities of tick-borne viruses (TBVs) from glands to saliva, advancing understanding of horizontal transmission risks for pathogens affecting human health.}, } @article {pmid40772864, year = {2025}, author = {Richter, TKS and Kauffman, M and Mammel, MK and Lacher, DW and Rajashekara, G and Leonard, SR}, title = {Long-term impacts of untreated dairy manure on the microbiome and Shiga toxin-producing Escherichia coli persistence in agricultural soil.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {9}, pages = {e0044725}, doi = {10.1128/aem.00447-25}, pmid = {40772864}, issn = {1098-5336}, mesh = {*Manure/microbiology/analysis ; *Soil Microbiology ; *Shiga-Toxigenic Escherichia coli/genetics/isolation & purification/physiology ; *Microbiota ; Animals ; Ohio ; Agriculture ; Soil/chemistry ; }, abstract = {Biological soil amendments of animal origin (BSAAO) improve the soil health of agricultural fields for plant growth. However, as natural reservoirs for bacterial foodborne pathogens, BSAAO application can introduce and support microbes of public health concern, such as pathogenic Shiga toxin-producing Escherichia coli (STEC), in agricultural soils. Using shotgun metagenomic sequencing, this project investigated the microbiome of soil with and without BSAAO, focusing on STEC and the E. coli population over time alongside changes in the soil microbiome and soil abiotic properties. Two farms in Ohio, one using an untreated dairy manure amendment and one that does not use a BSAAO, were sampled for over a year for metagenomic analysis of the soil microbiome. All manure samples were positive for stx genes, indicating the presence of STEC. Impacts of the manure on the soil lasted four weeks by several measures including higher E. coli diversity and more frequent STEC detection. Outside of these four weeks post-amendment, Shiga toxin genes (stx) were identified periodically in both fields throughout the year. STEC detection significantly correlated with higher in silico E. coli O-serogroup diversity, as well as lower soil cation exchange capacity and concentrations of calcium, magnesium, and organic nitrogen. Differential abundance analysis of the soil metagenomes identified several taxa influenced by amendment but did not identify taxa correlated with detection of stx genes. This work provides insights into the timing of and ecological factors associated with STEC persistence in the agricultural environment.IMPORTANCEShiga toxin-producing E. coli (STEC), including E. coli O157:H7, is a major etiological agent of foodborne human disease outbreaks associated with fresh produce and can be transferred to produce via contaminated agricultural soil. Given the devastating impacts of foodborne STEC outbreaks on public health and growers, it is necessary to understand the longevity of the impacts of manure application on the pathogen risk in the soil as well as better understand the ecological and environmental conditions that contribute to STEC survival in the agricultural soil environment. This work expands upon the knowledge of conditions that support STEC persistence in the produce-growing environment and its longevity following amendment in commercial fields with naturally occurring STEC contamination.}, } @article {pmid40772758, year = {2025}, author = {Yu, J-H and Lugli, GA and Ventura, M and van der Vaart, R and Nauta, A and Mahony, J and van Sinderen, D}, title = {Distinct shifts in bacteriophage diversity and abundance during various stages of Gouda-type cheese production.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {9}, pages = {e0065125}, doi = {10.1128/aem.00651-25}, pmid = {40772758}, issn = {1098-5336}, support = {EPSPG/2020/42//Irish Research Council/ ; 20/FFP-P/8864/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {*Cheese/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; Fermentation ; Phylogeny ; Genome, Viral ; *Lactococcus/virology ; Virome ; Food Microbiology ; }, abstract = {Bacteriophage (or phage) infection is known to disrupt milk fermentation processes involving lactic acid bacteria (LAB). This highlights the need to understand the dynamics of phage infection, particularly in fermentations involving undefined complex starter cultures, where conventional phage detection methodologies that rely on host bacteria come with limitations. Here, a metagenomic approach combined with microbiological methods was employed to assess the presence, diversity, and compositional changes in lactococcal phages within an industrial cheese production process. The virome data sets of ingredients and samples taken at various stages of the fermentation process were analyzed, revealing 12 presumptive lactococcal phage genomes belonging to either the Skunavirus genus or the P335 group phages. Phylogenetic analysis of the receptor-binding protein (RBP) sequence from these identified Skunavirus phages enabled us to predict the cell wall polysaccharide (CWPS) types of their bacterial hosts. This prediction was partially validated through host-range assays of three isolated phages, which matched phage genome contigs identified in the virome. Furthermore, alignment of their RBP-encoding gene sequences against virome data, along with real-time quantitative PCR targeting the Skunavirus genus, revealed a significant shift in the abundance and diversity of Skunavirus phages infecting different CWPS type strains throughout the production regime. Overall, our study revealed fluctuations in phage abundance and diversity during a cheese production cycle, underscoring the potential risk of inconsistent product quality due to phage proliferation and the need for effective strategies to mitigate phage contamination.IMPORTANCEThis study investigated dairy samples collected during a full fermentation cycle in a Gouda-type cheese facility to assess the prevalence, abundance, diversity, and dynamics of bacteriophages (phages) infecting starter culture components using a combination of metagenomic and microbiological assays. Also, by predicting the cell wall polysaccharide (CWPS) type of the host bacteria based on receptor-binding protein (RBP) sequences, the possible impact of bacteriophages on starter culture composition was evaluated. These findings highlight the need for tracking strategies to monitor bacteriophage dynamics in order to ensure robust and reliable fermentations.}, } @article {pmid40715814, year = {2025}, author = {Xiong, R and Aiken, E and Caldwell, R and Vernon, SD and Kozhaya, L and Gunter, C and Bateman, L and Unutmaz, D and Oh, J}, title = {AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.}, journal = {Nature medicine}, volume = {31}, number = {9}, pages = {2991-3001}, pmid = {40715814}, issn = {1546-170X}, support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; DP2 GM126893-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic/metabolism/microbiology/genetics/immunology/blood ; Male ; Female ; Metabolomics/methods ; Adult ; Biomarkers/blood/metabolism ; Gastrointestinal Microbiome/genetics ; Middle Aged ; *Artificial Intelligence ; Metabolome ; Neural Networks, Computer ; Longitudinal Studies ; Metagenomics ; Multiomics ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural network trained on a 4-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct a unique connectivity map spanning the microbiome, immune system and plasma metabolome in health and ME/CFS adjusted for age, gender and additional clinical factors. This map uncovers altered associations between microbial metabolism (for example, short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFN-γ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing unique mechanisms-specifically, how multi-omics dynamics are associated to the disease's heterogeneous symptoms.}, } @article {pmid40953029, year = {2025}, author = {Park, R and Chevalier, C and Kieser, S and Marizzoni, M and Paquis, A and Armand, S and Scheffler, M and Allali, G and Assal, F and Momjian, S and Frisoni, GB}, title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0330251}, pmid = {40953029}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Male ; Female ; Aged ; *Hydrocephalus, Normal Pressure/microbiology ; Alzheimer Disease/microbiology ; Aged, 80 and over ; Dysbiosis/microbiology ; Case-Control Studies ; Middle Aged ; }, abstract = {Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.}, } @article {pmid40948444, year = {2025}, author = {Bryson, S and Sisson, Z and Nelson, B and Grove, J and Reister, E and Liachko, I and Auch, B and Graiziger, C and Khoruts, A}, title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2559019}, doi = {10.1080/19490976.2025.2559019}, pmid = {40948444}, issn = {1949-0984}, mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteriophages/genetics/isolation & purification/classification ; *Plasmids/genetics ; Feces/microbiology/virology ; *Clostridium Infections/therapy/microbiology ; *Bacteria/genetics/classification/virology/isolation & purification ; Clostridioides difficile/genetics ; Male ; Female ; Middle Aged ; }, abstract = {Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.}, } @article {pmid40946204, year = {2025}, author = {Burnett, J and Buckley, D and Grinstead, DA and Oliver, HF}, title = {Microbial Community Associations With Listeria monocytogenes in Food Processing Environments: A Systematic Review and Meta-Analysis.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {5}, pages = {e70277}, pmid = {40946204}, issn = {1541-4337}, support = {//Diversey/ ; }, mesh = {*Listeria monocytogenes/growth & development/physiology/isolation & purification ; *Food Microbiology ; *Food Handling ; Microbiota ; Biofilms ; }, abstract = {Listeria monocytogenes persistence in food processing environments challenges current understanding of microbial community dynamics. This systematic review and meta-analysis examined peer-reviewed studies that screened for Listeria spp. and performed culture-independent metagenomics on FPE surface samples. Following PRISMA guidelines, we searched PubMed, Web of Science, and Food Science and Technology Abstracts databases, screening 464 studies, with 73 qualifying for full-text review. Seven studies met the inclusion criteria for final analysis, encompassing 1659 environmental samples from meat processing (n = 4 studies) and produce facilities (n = 3 studies). Meta-analysis using random effects models revealed no significant correlation between Listeria presence and overall microbial community alpha diversity (Shannon: z = -0.89, p = 0.40; inverse Simpson and Chao1 indices similarly non-significant). This finding challenges previous assumptions about the relationship between microbial diversity and pathogen persistence. Differential abundance analyses identified three genera most frequently associated with Listeria presence across multiple studies: Pseudomonas, Psychrobacter, and Acinetobacter. These Gammaproteobacteria are characterized as aerobic biofilm formers capable of growth at refrigeration temperatures. One study using rigorous mixed-effects modeling identified Veillonella as significantly associated with L. monocytogenes presence, suggesting potential anaerobic niche interactions within biofilm communities. Synthesis of metabolic capabilities reported in the literature suggests these associated genera may provide structural biofilm matrices and potentially complementary metabolic functions that could facilitate L. monocytogenes survival in FPE conditions. However, the genus-level resolution of 16S rRNA amplicon sequencing data and methodological variations across studies limit definitive conclusions about specific metabolic interactions. These findings indicate that L. monocytogenes persistence appears to be associated with specific microbial partners rather than overall community diversity metrics. Understanding these ecological relationships may inform targeted control strategies focusing on biofilm-forming genera that create favorable conditions for Listeria survival in food processing environments.}, } @article {pmid40944761, year = {2025}, author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U}, title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.}, journal = {Neurosurgical review}, volume = {48}, number = {1}, pages = {641}, pmid = {40944761}, issn = {1437-2320}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Adult ; *Brain Neoplasms/microbiology/metabolism ; Cross-Sectional Studies ; *Pituitary Neoplasms/microbiology/metabolism ; Aged ; }, abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.}, } @article {pmid40943581, year = {2025}, author = {Gałęcki, R and Nowak, A and Szulc, J}, title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, pmid = {40943581}, issn = {1422-0067}, support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; }, mesh = {Animals ; *Tenebrio/chemistry ; *Gastrointestinal Microbiome/genetics ; Rats ; Rats, Wistar ; *Metagenomics/methods ; *Animal Feed ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Male ; Feces/microbiology ; }, abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.}, } @article {pmid40943165, year = {2025}, author = {Wang, R and Ren, W and Liu, S and Li, Z and Li, L and Ma, S and Yao, X and Meng, J and Zeng, Y and Wang, J}, title = {Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, pmid = {40943165}, issn = {1422-0067}, support = {2022A02007-1 and ZYYD2025JD02.//Xinjiang Uygur Autonomous Region Major Science and Technology Special Project and the Central Guidance for Local Science and Technology Development Fund/ ; }, mesh = {Animals ; Horses ; *Gastrointestinal Microbiome/drug effects/genetics ; *Milk/metabolism ; *Metagenomics/methods ; Mice ; *Anti-Inflammatory Agents/pharmacology ; Female ; Cytokines/metabolism ; }, abstract = {This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods.}, } @article {pmid40897066, year = {2025}, author = {Slobodkina, GB and Merkel, AY and Kondrasheva, KV and Stroeva, AR and Bonch-Osmolovskaya, EA and Davranov, KD and Slobodkin, AI}, title = {Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {5}, pages = {126650}, doi = {10.1016/j.syapm.2025.126650}, pmid = {40897066}, issn = {1618-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Uzbekistan ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Metagenomics ; Metagenome ; *Rivers/microbiology ; *Bacteria/classification/genetics/metabolism ; Groundwater/microbiology ; *Microbiota ; Geologic Sediments/microbiology ; Hot Springs/microbiology ; }, abstract = {Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum[Ts] gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus[Ts] gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.}, } @article {pmid40882554, year = {2025}, author = {Balamurugan, J and Jagadeesan, H and Vijayakumar, M}, title = {A metagenomic approach to predict the role of microbiome in a plant-microbe system for degrading the model azo dye methyl red.}, journal = {Journal of contaminant hydrology}, volume = {275}, number = {}, pages = {104703}, doi = {10.1016/j.jconhyd.2025.104703}, pmid = {40882554}, issn = {1873-6009}, mesh = {*Azo Compounds/metabolism ; Biodegradation, Environmental ; *Microbiota ; Metagenomics ; *Plants/microbiology/metabolism ; *Coloring Agents/metabolism ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {Azo dye contamination poses significant environmental challenges due to its persistence and toxicity. Plant-microbe integrated systems offer a sustainable solution for dye bioremediation, yet the functional roles of microbial communities and their interactions within community and with host plants during bioremediation remain underexplored. This study presents an integrated, multi omics approach to dissect the microbial diversity, functional potential, and plant-microbe interactions within a plant-microbe integrated bioremediation system for model azo dye, methyl red degradation. The microbial diversity of various organisms enriched under different treatment conditions for effective azo dye treatment was explored. A read-based approach using HUMAnN 3 pipeline was adopted to extract metabolic information from the shotgun metagenomic reads. Diversity analysis showed the enrichment of microorganisms capable of growing in the presence of the pollutant methyl red in an oligotrophic condition. The metabolic potential of the enriched organisms in dye removal was studied. Based on the enzymatic abundance, a pathway for the degradation of methyl red is proposed. Endophytic bacteria such as Klebsiella pneumoniae and Klebsiella varicola were responsible for encoding major dye-degrading enzymes in plant-integrated systems. In the plant-microbe integrated system both endophytic and intestinal microorganisms such as Kluyvera intestini and Escherichia coli are among the top 5 contributors of genes encoding downstream aromatic compound degradation enzymes. Notably Enterococcus casseliflavus showed highest enzyme abundance for azobenzene reductase in plant -microbe integrated strategy with 11.5-fold greater abundance than the treatment system containing only microbial inoculum. Metabolomics data from root exudates experiment revealed the role of root exudates in selective recruitment of microbial community. The role of biofilm and quorum sensing pathways in enhancing the bioremediation potential of the microbiome and the potential microbe-microbe and plant-microbe interaction was analysed. Deciphering the metabolic contribution of each microorganism and the microbiome as a whole is crucial to design engineered bioremediation systems. ENVIRONMENTAL IMPLICATIONS: Understanding the potential of microorganisms, their enrichments, and survival will help in designing specific consortia for effective degradation of pollutants. Metagenomic analysis reveal that the functional complementation in the microbiome is responsible for the pollutant degradation and the presence of plants through the root exudates, provide the nutrients lacking in the oligotrophic conditions observed in many waste streams, thereby enriching suitable microorganisms. This metagenomic study along with the metabolomics component, provides the justification for the efficiency of the plant microbe treatment of model dye methyl red and this could be exploited in real time situations.}, } @article {pmid40880079, year = {2025}, author = {Tang, Y and Oliver, A and Alkan, Z and Korf, I and Huang, L and Kable, ME and Lemay, DG}, title = {Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults.}, journal = {Food & function}, volume = {16}, number = {18}, pages = {7393-7407}, doi = {10.1039/d5fo01640a}, pmid = {40880079}, issn = {2042-650X}, mesh = {Humans ; *Lactose/metabolism ; *Lactase/genetics/metabolism ; Male ; Female ; Adult ; Genotype ; Middle Aged ; Feces/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; United States ; Polymorphism, Single Nucleotide ; Yogurt ; Diet ; Lactose Intolerance/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; }, abstract = {Lactase persistence is a genetically inherited trait that enables continued lactose digestion into adulthood. Lactase non-persistence (LNP) individuals often experience incomplete lactose digestion, allowing undigested lactose to reach the colon, where it may shape microbial composition and function. We investigated the relationship between the lactase persistence (LP) genotype, lactose consumption, and the taxonomic and functional profiles of the fecal microbiome. Participants from the USDA Nutritional Phenotyping Study, a cross-sectional observational study designed to assess how dietary factors impact human health, whose fecal microbiome profile was measured using shotgun metagenomic sequencing (n = 330) were included in this analysis. Fecal SCFA levels were measured using GC-MS. Fecal microbiome taxonomy and gene abundance were quantified using shotgun metagenomic sequencing. Lactose consumption and yogurt intake were estimated based on Automated Self-Administered 24h Dietary Assessment Tool (ASA24®) dietary recalls or Food Frequency Questionnaire. The LP/LNP genotype was determined by a single nucleotide polymorphism (SNP ID: rs4988235). Several genera of lactic acid bacteria (Veillonella, Lactobacillus, Lacticaseibacillus, and Lactococcus) were differentially abundant between recent high-lactose consuming (>10.0 g lactose per day) and low-lactose consuming (<3.3 g lactose per day) individuals. Among the LNP participants who self-identified as Caucasian or Hispanic, high-lactose consumers (>10.0 g per day via 24-h recall) had significantly higher relative abundances of lactic acid bacteria and lactate-utilizing bacteria (Lacticaseibacillus, Lactobacillus, Megamonas, and Veillonella) than low-lactose consumers (<3.3 g per day). Independent of lactose intake, LNP participants had a higher abundance of fecal microbial β-galactosidase genes than LP participants. Among the LNP participants, those with high recent lactose consumption also showed a significant shift towards more fecal propionate. The abundance of the yogurt-associated microbe, Streptococcus thermophilus, was positively associated with yogurt intake independent of the genotype. Alternative milk consumption was significantly negatively associated with fecal SCFAs both in the full cohort and the Caucasian/Hispanic subset, regardless of the genotype. Our results suggest that functional and persistent host lactase enzymes may work to competitively exclude lactic acid bacteria, contributing to a smaller realized niche for lactic acid bacteria in LP individuals compared to LNP individuals. However, regardless of the host genotype, consumption of alternative milk may be associated with reduced production of health-promoting intestinal metabolites, such as SCFAs.}, } @article {pmid40855911, year = {2025}, author = {Wei, L and Wu, H and Wen, L and Chen, M and Cui, B and Wang, X and Wu, T and Cheng, Y}, title = {Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.}, journal = {Food & function}, volume = {16}, number = {18}, pages = {7266-7282}, doi = {10.1039/d5fo01536g}, pmid = {40855911}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Oryza/chemistry ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Male ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; *Peptides/pharmacology ; *Hyperlipidemias/metabolism/drug therapy ; *Plant Proteins/pharmacology/chemistry ; }, abstract = {Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.}, } @article {pmid40816065, year = {2025}, author = {Kim, E and Song, TC and Yang, SM and Kim, J and Kim, HY}, title = {Comparative analysis of microbial diversity and fatty acids in raw milk from different production systems.}, journal = {Food chemistry}, volume = {493}, number = {Pt 3}, pages = {145899}, doi = {10.1016/j.foodchem.2025.145899}, pmid = {40816065}, issn = {1873-7072}, mesh = {*Milk/microbiology/chemistry ; Animals ; *Fatty Acids/analysis/metabolism/chemistry ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Cattle ; Microbiota ; }, abstract = {This study investigated how differences in raw milk obtained from different milk production practices, such as conventional, antibiotic-free, and organic, influence microbial community structure and fatty acid profiles, potentially affecting milk quality. Microbial diversity revealed no significant differences among the three milk production practices. However, Pseudomonas was dominant across all milk types, with organic milk demonstrating significantly higher relative abundances of Lactococcus, Acinetobacter, and Carnobacterium. Fatty acid profiling revealed significantly higher levels of essential polyunsaturated fatty acids (PUFAs) in organic milk, probably due to easier access to pasture-based diets. Correlation and network analyses demonstrated associations between PUFAs and microbial genera predominantly present in organic milk, such as Serratia with C18:2n-6 and Lactococcus with C20:4n-6, suggesting a potential relationship between microbial composition and fatty acid metabolism influenced by production practices. These data emphasize the impact of production practices on milk quality and microbial dynamics.}, } @article {pmid40803134, year = {2025}, author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC}, title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.}, journal = {Microbiological research}, volume = {301}, number = {}, pages = {128299}, doi = {10.1016/j.micres.2025.128299}, pmid = {40803134}, issn = {1618-0623}, mesh = {*Wastewater/microbiology ; *Petroleum/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; China ; Metagenome ; Phylogeny ; Genome, Bacterial ; Nitrogen/metabolism ; Microbiota/genetics ; Biodegradation, Environmental ; Carbon/metabolism ; Metabolic Networks and Pathways/genetics ; CRISPR-Cas Systems ; }, abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.}, } @article {pmid40752126, year = {2025}, author = {Hong, W and Yang, S and Shu, W and Price, G and Song, L}, title = {Spatiotemporal dynamics of multi-kingdom microbiome interactions drive CNPS cycling in landfills.}, journal = {Waste management (New York, N.Y.)}, volume = {206}, number = {}, pages = {115048}, doi = {10.1016/j.wasman.2025.115048}, pmid = {40752126}, issn = {1879-2456}, mesh = {*Microbiota ; *Waste Disposal Facilities ; Phosphorus/metabolism/analysis ; Soil Microbiology ; Nitrogen/metabolism/analysis ; *Refuse Disposal ; Bacteria/metabolism ; Carbon/metabolism/analysis ; Solid Waste/analysis ; Sulfur/metabolism ; }, abstract = {Landfill ecosystems represent significant terrestrial carbon sinks, where municipal solid waste (MSW) undergoes decomposition and transformation through biochemical reactions mediated by multi-kingdom microbiome. However, the spatial and temporal characterization of microbial interactions and collaboration within these multi-kingdom microbiomes remain largely unknown. In this study, we reveal the hierarchical and collaborative mechanisms by which multi-kingdom microbiomes drive carbon, nitrogen, phosphorus, and sulfur cycling across a 30-meter landfilling depth, corresponding to a landfilling age of 1 to 4 years. Through integration of metagenomics and network analyses, we elucidated vertical succession patterns in microbial community structure and function. The surface layer (1-2 years) was centered on bacterial-dominated primary metabolism, with Enterococcus aquimarinus and Brevundimonas bullata inferred to mediate metabolic coupling through fermentation, nitrogen fixation andphosphorus solubilization. Concurrently, phage-driven host lysis may contribute to the suppression of acidification. In the middle layer (2-3 years), co-occurrence patterns between archaea and fungi suggest mutualistic interaction supporting methanogenesis, wherein fungi such as Anaeromyces robustus would supply key substrates for methanogens such as Methanofollis ethanolicus. In the bottom layer (3-4 years), fungi, bacteria, and viruses collaborate under nutrient-limited conditions, with phages employing a "kill-the-winner" approach to sustain ecosystem function and stability. Collectively, our findings indicate that key microbial connectors across kingdoms contribute to elemental cycling through cross-kingdom interaction, including substrate exchange and nutrient supply. This study advances our understanding of multi-kingdom microbial dynamics during MSW decomposition and offers a conceptual framework for enhancing biogeochemical cycling efficiency within landfill ecosystems.}, } @article {pmid40669611, year = {2025}, author = {Song, S and Li, F and Zhao, B and Xu, Y and Liu, Z and Liu, J and Hou, Q and Chen, J and Chen, M and Liu, Z and Zhou, M and Wu, X and Wang, X}, title = {Sparfloxacin ameliorates DSS-induced ulcerative colitis by suppressing cellular senescence, JAK/NF-κB signaling pathway and modulation of the gut microbiota-metabolite axis.}, journal = {Biochemical pharmacology}, volume = {241}, number = {}, pages = {117167}, doi = {10.1016/j.bcp.2025.117167}, pmid = {40669611}, issn = {1873-2968}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice ; *NF-kappa B/metabolism/antagonists & inhibitors ; *Cellular Senescence/drug effects/physiology ; *Fluoroquinolones/pharmacology/therapeutic use ; Signal Transduction/drug effects/physiology ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; Mice, Inbred C57BL ; *Dextran Sulfate/toxicity ; Male ; Humans ; }, abstract = {The progression of ulcerative colitis (UC) involves immune dysregulation, intestinal barrier dysfunction, and microbial dysbiosis while existing targeted therapies present challenges, including adverse effects and economic burdens. UC is characterized by persistent intestinal inflammation, manifesting as abdominal pain, hematochezia, and malnutrition. Prolonged uncontrolled inflammation may lead to colorectal cancer or severe complications, significantly impairing quality of life. Recent studies have revealed a significant correlation between pathological accumulation of senescent cells and UC pathogenesis, suggesting anti-senescence therapeutics as potential interventions. In this study, we identified sparfloxacin (SPA), a fluoroquinolone antibiotic, through high-throughput screening as an effective senolytic agent that markedly alleviates DSS-induced murine colitis. Mechanistically, combining cellular and animal experiments with transcriptomic, untargeted metabolomic, and metagenomic analyses, we demonstrated sparfloxacin's tripartite therapeutic effects: ① Senescence inhibition via downregulation of p16/p21 expression; ② Effective suppression of aberrant JAK/NF-κB signaling activation with a concomitant reduction in pro-inflammatory cytokines (TNF-α, IL-6); ③ Gut microbiota remodeling characterized by increased probiotic abundance and elevated levels of beneficial metabolites. This study for the first time elucidates the molecular mechanism whereby SPA ameliorates UC through coordinated multi-target actions involving senescence inhibition, anti-inflammatory effects, and microbiome restoration. Our findings not only expand the clinical applications of fluoroquinolones but also provide a theoretical foundation for developing integrated UC treatment strategies targeting cellular senescence.}, } @article {pmid40652650, year = {2025}, author = {Meng, X and Chen, S and Liu, Z and Cheng, L and Hu, Y and Huang, X}, title = {Mechanism of electro-acclimation shaped microbiota facilitating phosphorus release from iron-containing sludge: microbial reduction and induced dissolution.}, journal = {Water research}, volume = {286}, number = {}, pages = {124197}, doi = {10.1016/j.watres.2025.124197}, pmid = {40652650}, issn = {1879-2448}, mesh = {*Sewage/chemistry/microbiology ; *Phosphorus ; *Iron/chemistry ; *Microbiota ; Waste Disposal, Fluid ; Electrodes ; }, abstract = {Iron-based Chemically Enhanced Primary Treatment (Fe-CEPT) can efficiently concentrate phosphorus (P) from municipal wastewater into sludge; however, unfavorable P release efficiency impedes P recovery from Iron-based Chemically Enhanced Primary Sludge (Fe-CEPS). This study developed an electro-digester by applying controlled potentials to bio-electrodes. The electro-acclimated microorganisms on bio-electrodes achieved efficient P release due to microbial Fe(III) reduction and microbial metabolism-induced P-Fe complexes dissolution. In P release potential tests, 53.2 % of total P was released within 60 h after +1.0 V acclimation, 2.2-fold of the control. P fractionation analysis revealed that the proportion of Fe(II)-P, Fe(III)-P, and Reductant-P in Fe-CEPS (substrate) decreased by 9.7 %, 44.8 %, and 37.5 % after P release, respectively, combined with X-ray diffraction analysis, indicating P-release process followed Fe(III)-P and reductant-P first being reduced to Fe(II)-P and then dissolved into P(liquid), while inherent Fe(II)-P directly dissolved into P(liquid). The enhanced electron transfer capacity of electro-acclimated microorganisms, demonstrated by cyclic voltammetry analysis, promoted Fe(III)-P reduction. The lower pH (a minimum of 5.7) in mixed liquor, achieved by the enhanced metabolism of electro-acclimated microorganisms and elevated enzyme activities relating to hydrolysis-acidification, facilitated the dissolution of Fe(II)-P into the liquid phase. These two steps were dominated by enriched iron-reducing bacteria as Deferribacteraceae and fermentative bacteria as Clostridiaceae in electro-acclimation shaped microbiota. Metagenomic analysis showed consistent results as genes encoding cellular respiratory, metabolism and electron transportation upregulated significantly. These findings provided an eco-friendly, cost-effective solution for treating iron-containing chemical sludge and recovering valuable P resources.}, } @article {pmid40652649, year = {2025}, author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W}, title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.}, journal = {Water research}, volume = {286}, number = {}, pages = {124170}, doi = {10.1016/j.watres.2025.124170}, pmid = {40652649}, issn = {1879-2448}, mesh = {*Plastics ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; *Rivers/chemistry ; Biodegradation, Environmental ; Water Pollutants, Chemical ; Metals, Heavy ; }, abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.}, } @article {pmid40645053, year = {2025}, author = {Zhao, M and Xiong, S and Du, T and Xu, X and Li, H and Zhang, L and Xu, Y and Wei, T and Xiong, T and Xie, M}, title = {Elucidating microbial succession dynamics and flavor metabolite formation in korean style spicy cabbage fermentation: Integration of flavoromics, amplicon sequencing, and metagenomics.}, journal = {Food chemistry}, volume = {492}, number = {Pt 2}, pages = {145464}, doi = {10.1016/j.foodchem.2025.145464}, pmid = {40645053}, issn = {1873-7072}, mesh = {Fermentation ; *Flavoring Agents/metabolism/chemistry/analysis ; *Brassica/microbiology/chemistry/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Taste ; *Fungi/metabolism/genetics/classification/isolation & purification ; *Fermented Foods/microbiology/analysis ; Republic of Korea ; Volatile Organic Compounds/metabolism ; }, abstract = {Korean style spicy cabbage (KSC) is a prominent fermented vegetable consumed globally. Nevertheless, microbial succession dynamics, interactions, and flavor-core microbiome correlations lack comprehensive understanding. Metabolomics revealed eight taste-active compounds and sixteen aroma-active compounds as key flavor determinants throughout fermentation. Amplicon sequencing elucidated dynamic shifts in bacterial and fungal community structures during KSC fermentation, with subsequent analyses identifying free sugars as the primary drivers of microbial succession. Spearman correlation analysis further identified Psychrobacter, Latilactobacillus, Weissella, Pseudomonas, Rothia, Candida, Vishniacozyma, Kazachstania, and Cutaneotrichosporon as core microbes driving the formation of characteristic flavor metabolites in KSC. Through metagenomic analysis, we reconstructed the metabolic network underlying the formation of characteristic flavor compounds. Our study elucidates microbial diversity dynamics and flavor metabolite formation during KSC fermentation, offering actionable insights for identifying critical fermentation phases and optimizing inoculated starter culture.}, } @article {pmid40528807, year = {2025}, author = {Ding, X and Wang, J and Zhu, W}, title = {The hydrogenation metabolism process of rosmarinic acid by microbial enzymes in chickens.}, journal = {Journal of the science of food and agriculture}, volume = {105}, number = {13}, pages = {7340-7349}, doi = {10.1002/jsfa.70000}, pmid = {40528807}, issn = {1097-0010}, support = {2017YFE0135200//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Rosmarinic Acid ; *Chickens/microbiology/metabolism ; *Cinnamates/metabolism/chemistry ; *Depsides/metabolism/chemistry ; Gastrointestinal Microbiome ; Hydrogenation ; *Bacteria/genetics/enzymology/isolation & purification/classification/metabolism ; Tandem Mass Spectrometry ; *Bacterial Proteins/metabolism/genetics ; Gastrointestinal Tract/microbiology/metabolism ; }, abstract = {BACKGROUND: The gut microbiota plays a critical role in the metabolism of rosmarinic acid (RA) through converting RA to caffeic acid (CA), danshensu (DSS), and m-coumaric acid. However, the gut environment and microbiota may have complicated metabolic converting RA processes. This study aimed to investigate the metabolism of RA in gastrointestinal tract of chickens through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and metagenomic analysis.

RESULTS: Through in vivo and in vitro studies, RA was found to be hydrogenated into dihydrorosmarinic acid, then hydrolyzed into DSS and dihydrocaffeic acid (DHCA). DSS and DHCA could be further converted to 3-hydroxyphenylpropionic acid. But RA remained stable in the stomach, duodenum, jejunum, and ileum, as well as in the cecum of antibiotic-treated chickens. This indicated that the degradation of RA was mainly mediated by cecal microbiota. Furthermore, the metagenomic analysis of cecal microbiota revealed that reductases and hydrolases from Clostridium spp., Alistipes spp., and other microbiota were involved in these processes. NADH:flavin oxidoreductase and 3-oxoacyl-[acyl-carrier-protein] reductase participated in the hydrogenation reaction of RA, and BaiCD involved in dehydroxylation reaction of RA.

CONCLUSION: The hydrogenation process by microbial enzymes was an important metabolic pathway of RA. These hydrogenation products contribute to improving the biological function of RA. © 2025 Society of Chemical Industry.}, } @article {pmid40460824, year = {2025}, author = {Gogokhia, L and Tran, N and Grier, A and Nagayama, M and Xiang, G and Funez-dePagnier, G and Lavergne, A and Ericsson, C and Ben Maamar, S and Zhang, M and Battat, R and Scherl, E and Lukin, DJ and Longman, RS}, title = {Donor composition and fiber promote strain engraftment in a randomized controlled trial of fecal microbiota transplant for ulcerative colitis.}, journal = {Med (New York, N.Y.)}, volume = {6}, number = {9}, pages = {100707}, pmid = {40460824}, issn = {2666-6340}, support = {R01 DK128257/DK/NIDDK NIH HHS/United States ; T32 DK116970/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Colitis, Ulcerative/therapy/microbiology ; Male ; Female ; Double-Blind Method ; *Dietary Fiber/administration & dosage ; Adult ; Middle Aged ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Prebiotics ; Tissue Donors ; Psyllium/administration & dosage ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging treatment for ulcerative colitis (UC), but the impact of prebiotic fiber on FMT efficacy for UC is unclear. We performed a randomized, double-blind, placebo-controlled clinical trial to examine the efficacy of FMT with and without dietary fiber supplementation in patients with UC.

METHODS: 27 patients with mild to moderate UC were randomized to receive a single FMT or placebo with or without psyllium fiber supplementation for 8 weeks. The primary outcome was clinical response at week 8, and secondary outcomes included endoscopic improvement and clinical remission. Metagenomic sequencing of fecal DNA was analyzed to determine taxonomic profiles and donor strain engraftment.

FINDINGS: The trial was terminated early due to manufacturer discontinuation of FMT product. FMT induced clinical response, remission, and endoscopic improvement in UC patients compared to placebo (p < 0.05), but fiber did not improve clinical outcomes of FMT. Recipient microbiome composition post-FMT shifted toward donor composition in responders and non-responders, but the durability of this change was stronger in responders. Clinical response and durable change in microbiome composition following FMT was donor dependent. Strain tracking analysis also demonstrated a donor-dependent variability in the rate of successful engraftment and identified a consortium of engrafted bacteria associated with treatment response or fiber supplementation.

CONCLUSIONS: Single-dose FMT demonstrated clinical efficacy for mild to moderate UC compared to placebo but revealed no benefit of fiber supplementation. These results highlight proof of concept that donor selection and prebiotic fiber can shape strain-level engraftment. This study was registered at ClinicalTrials.gov: NCT03998488.

FUNDING: National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK128257, to R.S.L.).}, } @article {pmid40951316, year = {2025}, author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W}, title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1663666}, pmid = {40951316}, issn = {2235-2988}, abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.

METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.

RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.

CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.}, } @article {pmid40950593, year = {2025}, author = {Silva, ACP and Migliaccio, F and Barosa, B and Gallucci, L and Yücel, M and Foustoukos, D and Le Bris, N and Bartlett, SJ and D'Alessandro, V and Vetriani, C and Giovannelli, D}, title = {Hydrodynamic flow and benthic boundary layer interactions shape the microbial community in Milos shallow water hydrothermal vents.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1649514}, pmid = {40950593}, issn = {1664-302X}, abstract = {In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.}, } @article {pmid40943646, year = {2025}, author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A}, title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, pmid = {40943646}, issn = {1422-0067}, support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Bacteroides fragilis/genetics/isolation & purification ; Adult ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; *Hashimoto Disease/microbiology ; Young Adult ; Adolescent ; Aged ; Feces/microbiology ; Metagenomics/methods ; *Actinobacteria/genetics ; Case-Control Studies ; }, abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.}, } @article {pmid40938427, year = {2025}, author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D}, title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {10}, pages = {1112}, pmid = {40938427}, issn = {1573-2959}, support = {GSBTM/JD(R&D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; }, mesh = {*Wastewater/microbiology/chemistry ; *Rivers/microbiology ; *Bacteria/genetics/classification ; India ; *Environmental Monitoring ; *Drug Resistance, Bacterial ; Metagenomics ; Anti-Bacterial Agents/analysis ; Water Pollutants, Chemical/analysis ; *Water Microbiology ; *Microbiota ; }, abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.}, } @article {pmid40935093, year = {2025}, author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F}, title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.}, journal = {Travel medicine and infectious disease}, volume = {67}, number = {}, pages = {102901}, doi = {10.1016/j.tmaid.2025.102901}, pmid = {40935093}, issn = {1873-0442}, abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2%) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5%), followed by Giardia duodenalis (12.6%), Dientamoeba fragilis (7.5%), Cryptosporidium parvum (6.5%), and Entamoeba histolytica (4%). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.}, } @article {pmid40812303, year = {2025}, author = {Huang, Y and Zhang, X and Yu, C and Liu, Y and Kang, H and Liu, Y and Ni, Y and Xia, Y and Jiang, Z and Chen, J and Zhao, K and Han, L and Zou, X and Wang, J and Lei, T and Gan, C and Zhang, H}, title = {Lactobacillus acidophilus promotes cognitive function recovery via regulating microglial peroxisomal function in cerebral ischemia.}, journal = {Cell host & microbe}, volume = {33}, number = {9}, pages = {1484-1501.e12}, doi = {10.1016/j.chom.2025.07.018}, pmid = {40812303}, issn = {1934-6069}, mesh = {*Microglia/metabolism ; Animals ; *Lactobacillus acidophilus/physiology ; Mice ; Humans ; *Brain Ischemia/therapy/microbiology ; Gastrointestinal Microbiome ; *Peroxisomes/metabolism ; *Cognition/physiology ; Male ; Disease Models, Animal ; Probiotics ; Mice, Inbred C57BL ; Female ; Reactive Oxygen Species/metabolism ; Cognitive Dysfunction ; Middle Aged ; }, abstract = {Cerebral ischemia causes significant mortality and is accompanied by inflammatory reactions that exacerbate damage. While the gut microbiota is linked to clinical outcomes, specific treatments and mechanisms remain unclear. Our metagenomics linked low Lactobacillus abundance to cognitive decline in patients with cerebral ischemia. L. acidophilus supplementation alleviated post-ischemic deficits in murine middle cerebral artery occlusion and bilateral carotid artery stenosis models. The neuroprotective effects of L. acidophilus were driven by enhanced gut absorption of linoleic acid (LinA). L. acidophilus-induced LinA activates peroxisomes in microglia, triggering microglial reprogramming to an anti-inflammatory state via reactive oxygen species (ROS) scavenging and β-oxidation-mediated epigenetic changes. These L. acidophilus-driven effects are lost upon dietary deficits in LinA, microglia depletion, or peroxisome disruption. A randomized clinical trial showed that L. acidophilus improved cognition and cerebral blood flow in ischemic patients. This study was registered at ClinicalTrials.gov (NCT05845983). Collectively, these findings reveal a therapeutic axis whereby L. acidophilus drives microglial reprogramming, providing a basis for microbiome-targeted neurotherapies.}, } @article {pmid40669466, year = {2025}, author = {Ghiotto, G and Xirostylidou, A and Gaspari, M and Kougias, PG and Campanaro, S and Treu, L}, title = {Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.}, journal = {Cell genomics}, volume = {5}, number = {9}, pages = {100949}, doi = {10.1016/j.xgen.2025.100949}, pmid = {40669466}, issn = {2666-979X}, mesh = {*Metagenomics/methods ; Anaerobiosis ; *Ecosystem ; *Adaptation, Physiological/genetics ; *Microbiota/genetics ; *Methanobacteriaceae/genetics/metabolism ; Methane/metabolism ; Carbon Dioxide/metabolism ; Mutation ; }, abstract = {Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.}, } @article {pmid39672231, year = {2025}, author = {Luo, HY and Fang, J and Zhang, WH and Chan, KC and Chan, YM and Dong, CX and Li, SL and Lyu, AP and Xu, J}, title = {Dissecting the anti-obesity components of ginseng: How ginseng polysaccharides and ginsenosides target gut microbiota to suppress high-fat diet-induced obesity.}, journal = {Journal of advanced research}, volume = {75}, number = {}, pages = {811-828}, doi = {10.1016/j.jare.2024.12.002}, pmid = {39672231}, issn = {2090-1224}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Panax/chemistry ; *Ginsenosides/pharmacology/chemistry ; Diet, High-Fat/adverse effects ; *Obesity/drug therapy/etiology/microbiology/metabolism ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Anti-Obesity Agents/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Metagenomics ; }, abstract = {INTRODUCTION: Ginseng demonstrates therapeutic potential in treating obesity, with both experimental and clinical studies suggesting its anti-obesity effects are mediated by gut microbiota. Nonetheless, the specific chemical components responsible for this effect remain largely unidentified.

OBJECTIVES: This study aims to investigate the anti-obesity effects and mechanisms of ginseng polysaccharides (GP) and ginsenosides (GS), the primary chemical components of ginseng, with a focus on their impact on gut microbiota.

METHODS: The impact of GP and GS on high-fat diet (HFD)-induced obesity was assessed using a mouse model. Molecular mechanisms were explored through a combination of chemical analysis, metagenomics, RT-qPCR, ELISA, and biochemical assays.

RESULTS: GP or GS administration effectively prevented adiposity in HFD-fed mice, and both effects were mediated by gut microbiota. Chemical analysis revealed diverse glycosyl groups in GP and GS. Metagenomics data suggested that GP-enriched species, e.g., Bacteroides stercorirosoris and Clostridiales bacterium encoded carbohydrate-active enzymes GH35, GH43 and PL9_1, while GS-enriched Sulfurospirillum halorespirans encoded GH16_5. These enzymes facilitated the utilization of glycosyl groups in GP and GS, selectively stimulating bacterial growth and reshaping the gut microbiota. Furthermore, bacterial species enriched by GP or GS encoded specific functional genes involved in short-chain fatty acid (SCFA) synthesis (K00625 and K00925 for GP; K18118, K00100, and K18122 for GS) and intestinal gluconeogenesis (IGN) (K01678, K00024, and K01596 for GP; K18118 and K00278 for GS). Consequently, the SCFA-GLP-1/PYY signaling and IGN were activated by both GP and GS to ameliorate obesity phenotypes.

CONCLUSION: GP and GS, containing diverse glycosyl groups, selectively stimulate specific gut bacteria, triggering mechanisms involved in SCFA-GLP-1/PYY signaling and IGN activation to reduce adiposity in HFD-fed mice. The study enhances understanding of the chemical components crucial for the gut microbiota-mediated anti-obesity effect of ginseng. The mechanistic understanding provides valuable insights for developing ginseng-based drugs or health products to combat obesity.}, } @article {pmid40827090, year = {2025}, author = {Mulligan, C and Gold, DA}, title = {A Reassessment of the Coprostane Biomarker in the Ediacaran With Implications for Dickinsonia.}, journal = {Geobiology}, volume = {23}, number = {4}, pages = {e70029}, pmid = {40827090}, issn = {1472-4669}, support = {2044871//National Science Foundation/ ; }, mesh = {Animals ; *Fossils/microbiology ; Biomarkers/analysis ; *Cholestanes/analysis ; *Bacteria/genetics/metabolism ; Gastrointestinal Microbiome ; }, abstract = {The discovery of cholestane in animal fossils from the Ediacaran (571-541 million years ago) has generated much excitement, but it is not the only interesting biomarker recovered. Coprostane, a geologically stable form of coprostanol, has also been found in Ediacaran rocks. This is surprising, since coprostanol is typically used in modern settings as an environmental biomarker for humans and other mammals, who produce the compound with help from bacteria in their gut. The prevailing hypothesis is that an abundance of coprostane in some Ediacaran fossils-particularly Dickinsonia-represents the degradation of the organism's cholesterol by bacteria in the microbial mat, comparable to what is seen in modern vertebrate corpses as they decompose. However, this hypothesis assumes coprostanol-producing bacteria were absent in the guts of Ediacaran organisms, and to date no one has tested whether such bacteria exist in modern invertebrates. In this study, we assembled 115 metagenomes to look for evidence of coprostanol-producing enzymes in invertebrate microbiomes. Ultimately, we did not find any evidence for the enzyme in any invertebrate microbiomes, supporting the hypothesis that coprostane is not a gut biomarker for Ediacaran animals. However, a reassessment of coprostane/cholestane ratios shows Dickinsonia was unique in coprostanol enrichment, with ratio levels comparable to waste polluted marine waters and modern vertebrate feces. While we cannot rule out the possibility of contamination, we prefer a novel interpretation of the coprostane signature in dickinsoniomorph fossils, where the elevated level of coprostanol comes from digestion of the microbial mat and concentration of the biologically inert compound. If correct, the elevated coprostanol signal provides new insights into the feeding strategy of these enigmatic animals.}, } @article {pmid40826150, year = {2025}, author = {Dang, HT and Phung, TTB and Tran, DM and Bui, ATP and Vu, YH and Luong, MT and Nguyen, HM and Trinh, HT and Vo, HTN and Nguyen, TTT and Nguyen, AH and Tung, PD and Tran, LH and Van Nguyen, AT}, title = {High-dose multi-strain Bacillus probiotics enhance treatment and reduce antibiotic usage in children with persistent diarrhea through immune and microbiota modulation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {30231}, pmid = {40826150}, issn = {2045-2322}, support = {ANABIO/RG-2022-06//ANABIO R&D Ltd. Company, Viet Nam/ ; }, mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Diarrhea/microbiology/immunology/therapy/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Male ; Female ; Child, Preschool ; *Gastrointestinal Microbiome/drug effects ; *Bacillus ; Infant ; Double-Blind Method ; Child ; Treatment Outcome ; Cytokines/blood ; }, abstract = {Persistent diarrhea remains medical challenge to date regarding both its etiology and therapeutic interventions. Here, we conducted a randomized, double-blind, controlled clinical trial to evaluate the effectiveness of high-dose multi-strain Bacillus spore probiotics (LiveSpo DIA30) containing B. subtilis, B. clausii, and B. coagulans at 5 billion CFU/5 mL ampoule, in the supportive treatment of persistent diarrhea in children. Our findings revealed a significant 3-day shorter recovery period, 1.60-fold enhanced efficacy, and a 9.47-fold increase in odds (all p-values < 0.0001) for effectively resolving diarrhea by day 5 with the Bacillus spores. Notably, the group receiving LiveSpo DIA30 (Dia30 group) experienced a reduction in antibiotic treatment duration by 2 days compared to the Control group, equivalent to a 25% decrease in antibiotic usage. After 5 days of treatment, LiveSpo DIA30 demonstrated significant reductions in elevated blood pro-inflammatory cytokines, including IL-17 (26.62%; p = 0.0178), IL-23 (25.13%; p = 0.0256), TNF-α (19.09%; p = 0.038), and in fecal sIgA (24.24%; p = 0.0433). Analysis of 16S rRNA metagenome revealed that Dia30 group exhibited a notable increase in density of Actinomycetota and Bacillota phylum, along with Actinomycetaceae, Lactobacillaceae, and Streptococaceae families. Lacticaseibacillus rhamnosus, a beneficial gut species, was not detectable at day 0 but reached a density of 0.91% (p = 0.015) in Dia30 group by day 5. Additionally, Dia30 group showed a significant reduction in density of the Proteobacteria phylum, Enterobacteriaceae family, and harmful species Escherichia fergusoni (682.8-fold; p = 0.011). In conclusion, this clinical trial presents robust clinical evidence, supported by laboratory testing data, demonstrating the efficacy of multi-strain and high-concentration Bacillus spore probiotics in rapidly alleviating symptoms and reducing antibiotic usage in children with persistent diarrhea. This is archived by improving the native gut microbiota and modulating immunological responses.Trial registration: ClinicalTrials.gov, Identifier No: NCT05812820, 14/4/2023.}, } @article {pmid40825877, year = {2025}, author = {Xu, Y and Liu, Y and Leng, Y and Qian, J and Yang, Q and Zhu, J and Li, G and Peng, Y}, title = {Signature of oral microbial dysbiosis in different periodontitis risk levels.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {186}, pmid = {40825877}, issn = {1432-0614}, support = {XDYC-YLWS-2023-0048//Xingdian Talents Support Program/ ; 202401AU070088//Natural Science Foundation of Yunnan Province/ ; EYQ2024001//National Key Clinical Specialty Development Project of Pediatric Dentistry Division of China/ ; 202501AY070001-052//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202401AY070001-365//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; }, mesh = {Humans ; *Periodontitis/microbiology ; *Dysbiosis/microbiology ; Metagenomics ; Female ; *Microbiota ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification ; Saliva/microbiology ; Adult ; *Mouth/microbiology ; }, abstract = {Individuals categorized into distinct periodontitis risk levels often demonstrate substantial disparities not only in the likelihood of developing periodontitis but also in the rate at which the disease progresses. However, the oral microbial communities and their functional characteristics corresponding to different periodontitis risk levels remain to be further explored. Therefore, 52 subjects with periodontitis were selected and categorized into different periodontitis risk groups based on the periodontal risk calculator (PRC). Unstimulated saliva was collected, and metagenomics sequencing was performed to compare microbial diversity, taxonomy, and functional annotation among groups. There was no significant difference in species richness and evenness between the very high risk group and the high risk group, but beta diversity increased in the former group. A higher abundance of Filifactor alocis, Streptococcus cristatus, Klebsiella pneumoniae, and Streptococcus anginosus was attributed to the very high risk group, while Pseudopropionibacterium propionicum and Abiotrophia defectiva were found in higher abundance in the high risk group. Functional annotation revealed that biosynthesis of amino acids (lysine biosynthesis; phenylalanine, tyrosine and tryptophan biosynthesis; valine, leucine, and isoleucine biosynthesis), citrate cycle (TCA cycle), carbon fixation pathways in prokaryotes, oxidative phosphorylation, lipopolysaccharide biosynthesis, fatty acid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, pantothenate and CoA biosynthesis, and glutathione metabolism were enriched in the very high risk group. The combined results indicate that the periodontal pathogens associated with a higher risk of periodontitis and the regulation of their related functional pathways increase the risk and likelihood of periodontitis development. KEY POINTS : • There were differences in microbial diversity among different periodontitis risk-level groups. • Some previously overlooked species and pathogenic pathways were linked to periodontitis risk differences. • Combining PRC with metagenomic sequencing revealed more potential pathogens.}, } @article {pmid40823805, year = {2025}, author = {Kim, L and Lavrinienko, A and Sebechlebska, Z and Stoltenberg, S and Bokulich, NA}, title = {Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.}, journal = {Nucleic acids research}, volume = {53}, number = {15}, pages = {}, pmid = {40823805}, issn = {1362-4962}, support = {2020-2024//ETH Domain's Open Research Data (ORD)/ ; 2021-362//ETH Domain's Open Research Data (ORD)/ ; //Strategic Focus Area "Personalized Health and Related Technologies (PHRT)/ ; //ETH Zurich/ ; //ETH Read and Publish OA/ ; }, mesh = {*Metadata/standards ; Humans ; *Information Dissemination/methods ; *Microbiota/genetics ; Metagenome/genetics ; *Metagenomics/standards/methods ; Gastrointestinal Microbiome/genetics ; Software ; }, abstract = {Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in microbiome research and adjacent communities, we (i) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (ii) developed an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n = 2929) spanning human gut microbiome research, and case studies of soil and gut microbiota (n = 370), we found nearly half do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes (i) the ineffectiveness of sequence data availability statements and (ii) the lack of consistent metadata reporting. We highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate that our tiered badge framework will promote dialogue regarding data sharing practices and facilitate data reuse, supporting best practices that make microbiome data Findable, Accessible, Interoperable, and Reusable (FAIR).}, } @article {pmid40768422, year = {2025}, author = {Pan, S and Li, W and Zhao, X and Wang, H and Liu, J and Zhang, W and Zhou, C and Xie, Y}, title = {Blood virome profiling reveals subtype-specific viral signatures and reduced diversity in non-Hodgkin lymphoma.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2542457}, pmid = {40768422}, issn = {2150-5608}, mesh = {Humans ; *Virome ; *Lymphoma, Non-Hodgkin/virology/blood ; Middle Aged ; Male ; Female ; Aged ; Adult ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Aged, 80 and over ; }, abstract = {Non-Hodgkin lymphoma (NHL), a heterogeneous lymphoid malignancy, demonstrates molecular diversity linked to genetic and immune factors, with emerging roles for viral infections in pathogenesis. Yet, the blood virome's composition and dynamics in NHL remain poorly characterized. This study characterizes the blood virome in NHL subtypes using viral metagenomic sequencing of serum from 217 patients (B-cell: BCL, T-cell: TCL, NK-cell: NKCL) and 40 healthy controls. Bioinformatic analysis identified 45 viral families, revealing subtype-specific viromic signatures. BCL exhibited a dominance of Anelloviridae, which accounted for 86% of eukaryotic viruses, compared with only 3% in controls, correlating with immunosuppression. Additionally, picobirnavirus, an opportunistic pathogen particularly in hosts with compromised immune systems, also showed a significant difference compared to controls. NKCL showed Flaviviridae enrichment, accounting for 82% of eukaryotic viruses, with nearly all of them being human pegivirus-1 (HPgV-1). Compared with healthy controls, patients with NHL exhibited significantly lower blood virome α-diversity at the genus level, and T-cell lymphomas showed the lowest species-level richness (140 vs. 332 in controls). Beta diversity highlighted BCL-specific viral heterogeneity, contrasting conserved T/NKCL viral profiles. Anelloviridae and Picobirnavirus expansion aligns with immune dysfunction, whereas NKCL-restricted HPgV-1 prevalence underscores biomarker potential. These findings implicate blood virome alterations marked by viral family predominance and diversity loss in NHL pathogenesis via immune modulation or oncogenesis. This first comprehensive NHL virome profile identifies subtype-specific signatures (Anelloviridae/Picobirnavirus/HPgV-1) for potential diagnostic and therapeutic targeting. Validation of these biomarkers may refine NHL subtyping and elucidate virome-lymphomagenesis mechanisms.}, } @article {pmid40738105, year = {2025}, author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ}, title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.}, journal = {Cell host & microbe}, volume = {33}, number = {8}, pages = {1381-1395.e7}, pmid = {40738105}, issn = {1934-6069}, support = {DP2 AI154402/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Bacteriophages/physiology ; *Metagenomics ; Escherichia coli/virology/genetics ; *Bacteria/genetics/virology/classification ; Soil Microbiology ; *Metagenome ; }, abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defenses. Evidence suggests that many examples in nature have not been described. Using plasmid libraries expressing small DNA inserts and functional selections for antiphage defense in Escherichia coli, we identified over 200 putative defenses from 14 bacterial phyla in 9 human and soil microbiomes. Many defenses were unrecognizable based on sequence or predicted structure and thus could only be identified via functional assays. In mechanistic studies, we show that some defenses encode nucleases that distinguish phage DNA via diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of unknown defenses with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed. Collectively, these findings highlight the diversity and interoperability of antiphage defense systems.}, } @article {pmid40742180, year = {2025}, author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM}, title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0098425}, pmid = {40742180}, issn = {2379-5077}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 DK133468/DK/NIDDK NIH HHS/United States ; R01DK133468//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; Biomass ; *Bacteria/genetics/isolation & purification ; *Metagenome ; Animals ; Host Microbial Interactions/genetics ; }, abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, quantitative polymerase chain reaction (qPCR), or spike-ins, can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read count ratios. We compared B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. B:H ratios in stool were correlated with bacterial-to-diet (B:D) read count ratios, but B:D ratios exhibited a substantial number of outlier points. Host read depletion methods reduced the total number of human reads in a given sample, but B:H ratios were strongly correlated before and after host read depletion, indicating that host read depletion did not reduce the utility of B:H ratios. B:H ratios showed expected variation between health and disease states and were generally stable in healthy individuals over time. Finally, we showed how B:H and B:D ratios can be used to track antibiotic treatment response and recovery. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning, enabling robust absolute biomass estimates directly from stool metagenomic data.IMPORTANCEIn this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, additional experimental biomass measurements, or training data. The approach assumes that the contribution of host DNA to stool is more constant or stable than biologically relevant fluctuations in bacterial biomass. We find that host read normalization is an effective method for detecting variation in gut bacterial biomass. Absolute bacterial biomass is a key metric that often gets left out of gut microbiome studies, and empowering researchers to include this measure more broadly in their metagenomic analyses should serve to improve our understanding of host-microbiota interactions.}, } @article {pmid40742167, year = {2025}, author = {Fan, P and Ma, J and Shen, Q and Ouyang, Y and Zhang, T and Shen, J and Luo, Z-C and Liu, Z and Ouyang, F}, title = {Gut microbiota development, antibiotic resistome, and related perinatal factors in early infancy.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0050225}, pmid = {40742167}, issn = {2379-5077}, support = {81961128023,81673178//National Natural Science Foundation of China/ ; 2017YFE0124700//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Male ; Infant ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Bacteria/genetics/classification/drug effects ; Delivery, Obstetric ; Pregnancy ; *Drug Resistance, Microbial/genetics ; Cesarean Section ; }, abstract = {Early life is a critical window for gut microbiota development and antibiotic resistome. We aimed to investigate the microbiota longitudinal change during the first 6 months of life and the differences associated with assisted reproductive technology (ART) treatment, mode of delivery, and infant sex. Gut microbiota was measured by metagenomic sequencing of fecal samples repeatedly collected within 3 days after birth, at 42 days, 3 months, and 6 months in 155 Chinese infants. Among infants born by vaginal delivery, the ACE, Chao, and Sobs indexes increased with age. Accordingly, the relative abundance of Actinobacteria phylum increased from 43% ± 37% (mean ± SD) to 57% ± 36% and Proteobacteria phylum decreased from 48% ± 36% to 17% ± 25%; and Bifidobacterium and Klebsiella genus increased and Escherichia genus decreased, from the first 3 days to 6 months. The dominant antibiotic resistance genes were macB and msbA. Boys and girls had similar features. Infants born by cesarean section exhibited a similar gut microbiota developmental trajectory, but with a slower increase in alpha diversity over time, and lower Bacteroidetes phylum and Bacteroides genus at each age point. Compared with non-ART infants, ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. Our findings confirm increasing diversity and composition evolution of gut microbiota in the first 6 months of life. Both modes of delivery and ART conception are associated with early gut microbiota alteration.IMPORTANCEGut microbiota plays an important role in various aspects of human health. Early life is a critical period for the development of gut microbiota. In this prospective study, we observed that the diversity and antibiotic resistance genes of gut microbiota increased gradually with age in the first 6 months of life. Boys and girls had similar features of gut microbiota. Cesarean section was associated with a lower abundance of Bacteroidetes phylum and Bacteroides genus. Compared with non-ART infants (spontaneous conception), ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. This study presents gut microbiota development with age, antibiotic resistome, and related perinatal factors in early infancy.}, } @article {pmid40698936, year = {2025}, author = {Maghini, DG and Kiguchi, Y and Darling, AE and Monahan, LG and Halpern, AL and Burke, CM and Jaeger, E and Statham, A and Truong, T and Ying, K and Bruinsma, SP and Schroth, GP and Bhatt, AS}, title = {Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0153124}, pmid = {40698936}, issn = {2379-5077}, support = {//Stand Up To Cancer/ ; //Allen Foundation/ ; //Stanford Medicine Children's Health Center for IBD and Celiac Disease/ ; R01 AI143757/AI/NIAID NIH HHS/United States ; //Chan Zuckerberg Initiative/ ; P30 CA124435, R01 AI143757, 1S10OD02014101, R01 AI148623/NH/NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; //Alfred P. Sloan Foundation/ ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial/genetics ; *Metagenomics/methods ; *Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; Nanopore Sequencing ; }, abstract = {Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches require high DNA input and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics for the first time. We sequenced a microbial mock community and 10 human gut microbiome samples with standard, shotgun 2 × 150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 ± 24.8 kilobases) than short read assemblies (9.9 ± 4.5 kilobases; P = 0.002), and comparable N50 to nanopore assemblies (91.0 ± 43.8 kilobases; P = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% ± 20.6%) than nanopore draft genomes (85.9% ± 23.0%; P ≤ 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 ± 114.7 base pairs) relative to ICLR genomes (954.6 ± 71.5 base pairs; P ≤ 0.001). Overall, we find that ICLR sequencing is a promising method for the accurate assembly of microbial genomes from gut metagenomes.IMPORTANCEMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to high input requirements. A new method, the Illumina Complete Long Read (ICLR) assay, is capable of generating highly accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents an additional option for assembling complete genomes from complex metagenomes.}, } @article {pmid40643235, year = {2025}, author = {Wang, X and Lv, Y and Zhao, W and Xiao, X and Wang, J}, title = {D-amino acid metabolic versatility as a common adaptive strategy in the Mariana Trench microbiome.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0058125}, pmid = {40643235}, issn = {2379-5077}, mesh = {*Amino Acids/metabolism ; *Microbiota/genetics ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; Geologic Sediments/microbiology ; Seawater/microbiology ; Ammonia/metabolism ; Carbon/metabolism ; Metagenomics ; }, abstract = {UNLABELLED: Hadal trenches, the Earth's deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions.

IMPORTANCE: Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.}, } @article {pmid40631858, year = {2025}, author = {Qu, S and Gu, Y and Hou, X and Wei, M and Wang, M and Su, Y and Miao, Y and Yang, J and Sun, Y and Zeng, Z}, title = {Dual associations of gut and oral microbial networks with kidney transplantation.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0025225}, pmid = {40631858}, issn = {2379-5077}, support = {82200679, 8246030754//National Natural Science Foundation of China/ ; 202201AW070019//Applied Basic Research Foundation of Yunnan Province/ ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Saliva/microbiology ; Female ; Male ; Feces/microbiology ; Middle Aged ; Metagenomics/methods ; *Mouth/microbiology ; Adult ; Kidney Failure, Chronic/microbiology/surgery ; *Microbiota ; }, abstract = {UNLABELLED: Gut and oral microbiomes play an essential role in the occurrence and development of kidney disease, but their changes after kidney transplantation in patients with end-stage renal disease and their relationships with host health remain unclear. Through shotgun metagenomic sequencing of fecal and saliva samples, we found that for both gut and oral microbiome, the initial loss of species diversity after kidney transplantation led to a reduction in network nodes and interactions, but strengthened the connections among the remaining species, which started to get a recovery approximately 7-14 days later. Different network modules tended to exhibit unique functions and showed different responses to transplantation. These network changes were significantly correlated with clinical indicators, especially with estimated glomerular filtration rate, suggesting that microbial networks contributed to regulating kidney function and host health from dual dimensions. Our study provides novel insights into associating microbiomes with patient recovery after kidney transplantation and offers new diagnostic strategies.

IMPORTANCE: Understanding the dynamics of gut and oral microbiomes after kidney transplantation is crucial for improving post-transplant outcomes and managing potential complications. Through shotgun metagenomic sequencing of fecal and saliva samples from patients following kidney transplantation, our study emphasizes that, in addition to focusing on the various microbial species themselves, the topological properties of gut and oral microbial networks are also critically important for kidney function. We aim to explore the relationship between host health and the oral and gut microbiomes following kidney transplantation from an ecological perspective and extend to other diseases to advance the study of the microbiome and its clinical impact.}, } @article {pmid40626735, year = {2025}, author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA}, title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.}, journal = {mSystems}, volume = {10}, number = {8}, pages = {e0174424}, pmid = {40626735}, issn = {2379-5077}, support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Microbiota/genetics ; *Metagenome/genetics ; Metagenomics/methods ; Ecosystem ; }, abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.

IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.}, } @article {pmid40489796, year = {2025}, author = {Andersen, S and Kennedy, G and Banks, M and Flanagan, B and Henden, A}, title = {Prebiotic fiber enteral supplementation after allogeneic transplantation: feasibility and impact on the microbiome.}, journal = {Blood advances}, volume = {9}, number = {16}, pages = {4167-4179}, pmid = {40489796}, issn = {2473-9537}, mesh = {Humans ; *Prebiotics/administration & dosage ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Female ; Male ; Middle Aged ; *Enteral Nutrition/methods ; Transplantation, Homologous ; *Gastrointestinal Microbiome ; Adult ; *Dietary Fiber/administration & dosage ; Pilot Projects ; }, abstract = {The decline in diversity of the gastrointestinal microbiome during hematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. Although provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fiber-containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome, and metabolomic outcomes between patients who received standard EN (n = 10) vs prebiotic fiber EN (n = 20) after allogeneic HSCT. Stool samples were collected at baseline and at periengraftment and were analyzed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fiber intake after transplant to an average 22 g/d compared with 4 g/d in the standard-care group. High tolerance of both EN formulas was observed with only 20% (n = 2) of the standard and 15% of the prebiotic group (n = 3) requiring parenteral nutrition (P = 1.0). There was no difference in the amount of EN provided, EN duration, or clinical outcomes. Microbial diversity declined in both groups with no difference post-EN provision (P = .93), however, there was a significant difference in relative abundance of Lactobacillus_C rhamnosus, with an increase in the prebiotic group only (P = .022). The relative abundance of Faecalicatena gnavus increased in the standard group and declined in the prebiotic group (P = .0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only after EN provision (P = .00035). A longer fiber intervention should be trialed to optimize clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as #ACTRN12621000832875.}, } @article {pmid40933366, year = {2025}, author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR}, title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.}, journal = {PNAS nexus}, volume = {4}, number = {9}, pages = {pgaf260}, doi = {10.1093/pnasnexus/pgaf260}, pmid = {40933366}, issn = {2752-6542}, abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.}, } @article {pmid40931350, year = {2025}, author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T}, title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {276}, pmid = {40931350}, issn = {1474-760X}, support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; }, abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .}, } @article {pmid40929115, year = {2025}, author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE}, title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331736}, pmid = {40929115}, issn = {1932-6203}, mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; }, abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.}, } @article {pmid40765405, year = {2025}, author = {Dai, G and Zhang, Y and Shen, C and Jiao, Y and Shen, W and Yu, F and Liu, R and Wang, D and Yuan, G and Jia, J}, title = {Luteolin Treats Obese Rats With Polycystic Ovary Syndrome by Improving Liver Lipid Metabolism and Regulating the Gut Microbiota.}, journal = {Phytotherapy research : PTR}, volume = {39}, number = {9}, pages = {4171-4180}, doi = {10.1002/ptr.70043}, pmid = {40765405}, issn = {1099-1573}, support = {JLY2021209//Clinical Medical Science and Technology Development Foundation of Jiangsu University/ ; BK20231251//Natural Science Foundation of Jiangsu Province/ ; JDY2022005//Key project for Medical Education Collaborative Innovation Fund of Jiangsu University/ ; BE2023757//Social Development Project of Jiangsu Province/ ; BRA2022008//the sixth phase 333 second level talent training project of Jiangsu Province (tackling bottleneck technology)/ ; jdfyRC2020010//Doctoral Research Initiation Fund/ ; BGYCA202207//Beigu Talent Cultivation Program of Affiliated Hospital of Jiangsu University/ ; SS202204-KFB05//open project of clinical medical research center of Gynecology and Traditional Chinese Medicine of Zhenjiang/ ; MS2024142//Science and Technology Development Program for Traditional Chinese Medicine of Jiangsu Province/ ; }, mesh = {Animals ; *Luteolin/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Polycystic Ovary Syndrome/drug therapy/complications/metabolism ; *Obesity/drug therapy/complications ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Rats ; Rats, Sprague-Dawley ; Body Weight/drug effects ; Disease Models, Animal ; }, abstract = {Polycystic ovary syndrome (PCOS) and obesity share a bidirectional relationship. While previous studies have indicated the anti-obesity effects of luteolin, its role in PCOS exacerbated by obesity remains unclear. This study aimed to investigate the ameliorative effects of luteolin on obese rats with PCOS and explore its underlying mechanisms. We established a rat model of PCOS with obesity and administered luteolin to evaluate its mitigating effects on the metabolic phenotype. Liver transcriptomics and fecal metagenomics were employed to analyze potential targets and alterations in the gut microbiota composition associated with luteolin's effects. Results showed that luteolin reduced body weight, improved estrous cycles, polycystic ovarian morphology, and glucose tolerance, and lowered serum levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-c) in the model rats. Importantly, luteolin significantly alleviated hepatic steatosis and reversed the expression of 138 key differentially expressed genes (DEGs) in the liver, including UQCRC2, IRS2, NFIX, and ALDH6A1. In addition, luteolin significantly increased the alpha diversity of the gut microbiota and modulated its composition, specifically increasing the relative abundance of Bacteroidota and decreasing that of Firmicutes. Our findings suggest that luteolin exerts beneficial effects on PCOS with obesity, potentially mediated through the improvement of hepatic lipid metabolism and the restoration of gut microbiota homeostasis. Luteolin emerges as a promising therapeutic candidate for managing PCOS with obesity.}, } @article {pmid40689619, year = {2025}, author = {Tambovtseva, RS and Arslan, LA and Grigoryeva, TA and Abdulkhakov, SR and Doludin, YV and Stoma, IO and Rizvanov, AA and Miftakhova, RR and Gabdoulkhakova, AG}, title = {Narrative review on bacteria-derived metabolites in the pathogenesis of ulcerative colitis.}, journal = {Clinical microbiology reviews}, volume = {38}, number = {3}, pages = {e0021024}, pmid = {40689619}, issn = {1098-6618}, support = {FZSM-2023-0011//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Colitis, Ulcerative/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/metabolism ; }, abstract = {SUMMARYThe pathogenesis of ulcerative colitis (UC) is heterogeneous; the causes are considered to be external factors such as stress, infections, antibiotics, and other medications, diet, and intrinsic factors such as genetic predisposition. The aim of this narrative review is to analyze data on intestinal flora and bacteria-derived metabolites in inflammatory bowel diseases and ulcerative colitis in particular. The main focus is on proteolytic, saccharolytic, mucin-degrading, and bile acid-metabolizing bacteria. What types of metabolites are beneficial for intestinal integrity and the patient's health? How can dietary preferences trigger disease and cause complications? What kind of changes in the microbiome promote the disease? We consider what targets/receptors metabolites act on and their physiological role. The knowledge accumulated over the past years on the gut metagenome, metabolome, and signaling mechanisms may allow, in the future, modulating the composition of the intestinal microbiome and suppressing the growth of pathogenic flora without the use of antibiotics, but due to pro- and prebiotics, products of bacterial metabolism, including quorum sensing molecules.}, } @article {pmid40927879, year = {2025}, author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C}, title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70096}, doi = {10.1111/mec.70096}, pmid = {40927879}, issn = {1365-294X}, support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; }, abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.}, } @article {pmid40927726, year = {2025}, author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN}, title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1575452}, pmid = {40927726}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; }, abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.}, } @article {pmid40926344, year = {2025}, author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P}, title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70190}, doi = {10.1111/1758-2229.70190}, pmid = {40926344}, issn = {1758-2229}, support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; }, mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation & purification ; Plant Leaves/parasitology ; }, abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.}, } @article {pmid40924621, year = {2025}, author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C}, title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c09633}, pmid = {40924621}, issn = {1520-5851}, abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.}, } @article {pmid40793781, year = {2025}, author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA}, title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.}, journal = {mBio}, volume = {16}, number = {9}, pages = {e0113425}, doi = {10.1128/mbio.01134-25}, pmid = {40793781}, issn = {2150-7511}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *DNA Transposable Elements ; Feces/microbiology ; Ecuador ; Metagenomics ; Child ; Child, Preschool ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Female ; Gene Transfer, Horizontal ; Male ; Plasmids/genetics ; }, abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.}, } @article {pmid40779866, year = {2025}, author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ}, title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139382}, doi = {10.1016/j.jhazmat.2025.139382}, pmid = {40779866}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics & numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics & numerical data ; Wetlands ; Electrochemical Techniques ; }, abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.}, } @article {pmid40671669, year = {2025}, author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Estévez, M}, title = {Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {36}, pages = {22698-22713}, doi = {10.1021/acs.jafc.5c02799}, pmid = {40671669}, issn = {1520-5118}, mesh = {Animals ; Rats, Wistar ; Rats ; *Gastrointestinal Microbiome ; Male ; *Biomarkers/urine/blood ; Bacteria/classification/isolation & purification/genetics/metabolism ; Triticum/metabolism ; *Meat/analysis ; Cattle ; Humans ; Urine/chemistry ; Glycine max/metabolism ; }, abstract = {Growing concerns about the alleged negative outcomes of the consumption of animal-based foods (ABF) lead a number of consumers to demand so-called plant-based meat analogues (PBMAs), which are designed to replicate the sensory and nutritional characteristics of genuine meat. This study aimed to characterize the physiological effects of long-term PBMA consumption by comparing their specific influence on both gut microbiota and fluids (i.e., plasma and urine) with those of conventional beef in a rodent model by using metagenomic and metabolomic tools. Twenty-one Wistar rats were divided into groups and consumed diets made with either wheat- and soy-based meat analogues or beef. The microbiota of PBMA-fed animals showed increased amounts of the harmful genus of gut bacteria, while their metabolomes reflected disturbances in the nitrogen-containing compound metabolism and the presence of potentially harmful metabolites. These results should raise concern and prompt further research into the long-term impact of consumption of PBMAs on health.}, } @article {pmid40923121, year = {2025}, author = {Li, Z and Zhao, K and Liu, H and Liu, J and Chen, X and Hu, W and Wen, E and Zhang, K and Chen, L}, title = {Construction of Predictive Machine Learning Model of Glioma-Associated Gut Microbiota.}, journal = {Brain and behavior}, volume = {15}, number = {9}, pages = {e70843}, doi = {10.1002/brb3.70843}, pmid = {40923121}, issn = {2162-3279}, support = {W2024SNKT13//the Research on Neurological Diseases and Nutritional Health at the Capacity Building and Continuing Education Center of the National Health Commission of China/ ; 82172680//the National Natural Science Foundation of China/ ; 82303586//the National Natural Science Foundation of China/ ; 82373220//the National Natural Science Foundation of China/ ; 82473264//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/physiology/genetics ; *Glioma/microbiology/diagnosis ; *Brain Neoplasms/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in the development of glioma. With the evolution of artificial intelligence technology, applying AI to analyze the vast amount of data from the gut microbiome indicates the potential that artificial intelligence and computational biology hold in transforming medical diagnostics and personalized medicine.

METHODS: We conducted metagenomic sequencing on stool samples from 42 patients diagnosed with glioma after operation and 30 non-intracranial tumor patients and developed a Gradient Boosting Machine (GBM) machine learning model to predict the glioma patients based on the gut microbiome data.

RESULTS: The AUC-ROC for the GBM model was 0.79, indicating a good level of discriminative ability.

CONCLUSIONS: This method's efficacy in discriminating between glioma cells and normal controls underscores the potential of machine learning models in leveraging large datasets for clinical insights.}, } @article {pmid40922218, year = {2025}, author = {Di Gianvito, P and Englezos, V and Ferrocino, I and Cocolin, L and Rantsiou, K}, title = {Survey of a grapevine microbiome through functional metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {219}, number = {}, pages = {117000}, doi = {10.1016/j.foodres.2025.117000}, pmid = {40922218}, issn = {1873-7145}, mesh = {*Vitis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Rhizosphere ; Fruit/microbiology ; Plant Leaves/microbiology ; }, abstract = {Microorganisms colonizing grapevines possess diverse functional capabilities that influence the health, growth, productivity and, consequently, wine quality. In this study, spatial and temporal dynamics of the microbiome of Vitis vinifera cv. Barbera grapevine were determined by shotgun sequencing. Bacterial and fungal populations and functions were monitored in samples of rhizosphere, leaves, and grapes, collected at different stages from fruit development to harvest in a conventionally managed vineyard. A compartmental specificity of diverse species was observed within both bacterial and fungal communities. A core microbiome was also identified. LEfSe analysis revealed significantly discriminant taxa associated with each plant compartment, but not according to the sampling time. KEGG genes associated with carbohydrate metabolism were the most abundant in all samples, followed by genes related to amino acid metabolism, respectively involved in carbon and nitrogen metabolic pathways. Interestingly, differences were observed in the functions of rhizosphere and phyllosphere communities with additional differences observed between functions of bacterial and fungal communities. Pathways involved in critical functions like nutrient acquisition, stress resistance, metabolic flexibility, and interaction with the grapevine, were detected within the microbiome. The findings of this study unravel ecological and functional characteristics of the Barbera microbiome. This fundamental understanding is a prerequisite for the development of tailored strategies to protect vineyards and promote sustainability in grapevine production.}, } @article {pmid40922213, year = {2025}, author = {Zhang, Z and Guo, Z and Cao, L and Hou, Q and Liu, Z and Zhong, J and Liu, N and Mei, X and Wang, Y}, title = {Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {219}, number = {}, pages = {116992}, doi = {10.1016/j.foodres.2025.116992}, pmid = {40922213}, issn = {1873-7145}, mesh = {*Taste ; *Fruit/microbiology/chemistry ; Odorants/analysis ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; Humans ; Amino Acids/analysis ; Metagenomics ; }, abstract = {Houhuo Daqu (HHD) exhibits significant heterogeneity between its core and peel layers, yet their differences remain underexplored. This study integrates metagenomic sequencing and electronic sensory technologies to compare the physicochemical properties, microbial communities, and flavor profiles of HHD's core and peel. Results reveal distinct microbial communities and diversity between the layers. Both are dominated by bacteria (>90 % relative abundance). The core shows significantly higher relative abundance of Bacillus licheniformis, Bacillus haynesii, and Bacillus paralicheniformis, while the peel has elevated levels of Streptomyces sp. NHF165, Pantoea agglomerans, and Lactiplantibacillus plantarum. Bacillus licheniformis is linked to acetic acid biosynthesis. Flavor analysis indicates both layers are rich in pyrazines, contributing to HHD's distinctive aroma. Enzyme activities differed markedly between the core and peel. Structural equation modeling, regression, and ENVFIT analyses show that amino acid nitrogen directly influences enzymatic activity and indirectly affects it by shaping microbial community and diversity. Additionally, amino acid nitrogen significantly impacts HHD's taste and aroma, modulated by starch and ash content. These findings highlight amino acid nitrogen as a key factor for controlling HHD quality in future production.}, } @article {pmid40922105, year = {2025}, author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C}, title = {Plastic-Microbial BioRemediation DB: A Curated Database for Multi-Omics Applications.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70178}, doi = {10.1111/1758-2229.70178}, pmid = {40922105}, issn = {1758-2229}, mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Soil Microbiology ; Metagenome ; Genomics ; Multiomics ; }, abstract = {Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.}, } @article {pmid40920777, year = {2025}, author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A}, title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331692}, pmid = {40920777}, issn = {1932-6203}, mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; }, abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.

METHODS: We collected plasma, serum, and stool samples from 123 adult patients with stable chronic HF and left ventricular ejection fraction (LVEF) ≤40%, and healthy controls (plasma: n = 51, stool samples: n = 69). Metabolomic and lipidomic profiling of plasma was performed using liquid chromatography with tandem mass spectrometry. Principal component analysis was used to explore differences in circulating profiles. Over-representation analysis was performed to identify pathways in which relevant metabolites were involved. Stool samples were sequenced using shotgun metagenomics. We calculated a dysbiosis index based on differential abundances of microbial taxa in patients vs. controls.

RESULTS: After adjusting for age, sex, and sampling location, we identified 67 enriched metabolites and 24 enriched lipids, and 115 depleted metabolites and 6 depleted lipids in HF patients compared to healthy controls. LVEF, N-terminal pro B-type natriuretic peptide, gut leakage markers, dysbiosis index, and fiber intake were not significantly related to any of the differentially abundant metabolites or lipids. Pathways related to energy metabolism differed most between HF patients and controls, however medication adjustment abolished all differences in circulating profiles.

CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.}, } @article {pmid40795725, year = {2025}, author = {Zhang, FL and Li, AY and Zhu, KX and Zhang, K and Tian, Z and Wang, T and Zhang, XH and Zang, J and Sun, XF and Shen, W and Li, L}, title = {Integrated multi-omics analysis uncovers Zearalenone-induced ovarian and intestinal inflammation is mediated by the tumor necrosis factor-α.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139476}, doi = {10.1016/j.jhazmat.2025.139476}, pmid = {40795725}, issn = {1873-3336}, mesh = {*Zearalenone/toxicity ; Animals ; Female ; *Tumor Necrosis Factor-alpha/genetics/metabolism ; *Inflammation/chemically induced/metabolism/genetics ; *Ovary/drug effects/pathology/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects/pathology ; Mice, Knockout ; Mice, Inbred C57BL ; Dysbiosis/chemically induced ; Cell Line ; Multiomics ; }, abstract = {As a widely encountered foodborne mycotoxin, Zearalenone (ZEN) has the potential to accumulate along the food chain, posing threats to public health and safety. However, the precise mechanisms by which ZEN causes tissue damage remain incompletely understood. Here, we established in vivo (40 μg/kg) and in vitro (30 μM) models to elucidate the underlying processes of ZEN-induced damage to the ovary and intestine. Our results demonstrated that, following ZEN exposure, pro-inflammatory signaling factors, including NLR family pyrin domain containing 3 (NLRP3) and Interleukin 6 (IL6), were significantly elevated in both ovarian and intestines. Metagenomic analysis revealed dysbiosis of the gut microbiota, which was closely associated with tumor necrosis factor (TNF)-α signaling pathway. Transcriptomic results further indicated that inflammatory response are intricately linked to TNF signaling pathway. Additionally, the Tnf-α knockout mouse model showed a marked resistance to ZEN-induced ovarian and intestinal injuries. In vitro, RNA interference targeting TNF-α attenuated the inflammatory response in IPEC-J2 cells. Moreover, dysregulated expression of the hormone synthesis genes, including KISS-1 metastasis suppressor (Kiss1) and gonadotropin releasing hormone 1 (Gnrh1), was observed, suggesting that ZEN-induced microbial dysbiosis and ovary damage may be interconnected through hormonal disruption. In summary, our results emphasize the role of TNF-α in causing ovarian and intestinal damage after ZEN exposure.}, } @article {pmid40752173, year = {2025}, author = {Li, WJ and Ghaly, TM and Tetu, SG and Huang, FY and Li, HZ and Li, H}, title = {Effects of agricultural inputs on soil virome-associated antibiotic resistance and virulence: A focus on manure, microplastic and pesticide.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139380}, doi = {10.1016/j.jhazmat.2025.139380}, pmid = {40752173}, issn = {1873-3336}, mesh = {*Manure ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Pesticides/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Virome/drug effects ; Agriculture ; Virulence/genetics ; Virulence Factors/genetics ; Bacteria/genetics ; Soil/chemistry ; }, abstract = {Soil viruses are increasingly recognized as crucial mediators of horizontal gene transfer, yet their role in disseminating antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) under agricultural disturbances remains poorly understood. Here, we characterized the viromes and associated ARGs and VFGs in agricultural soils treated with low- and high-dose manures, microplastics, and pesticides. Using metagenomic sequencing coupled with advanced viral identification tools, we found that manure fertilization markedly altered viral community composition and increased viral diversity. Manure also enhanced the abundance of ARGs and VFGs in viromes by 2.0-9.8-fold and 2.0-8.1-fold, respectively, while microplastics and pesticides had limited impacts. Additionally, gene pathways related to human diseases and environmental adaptation were enriched in soil viromes treated with manures and high-dose pesticides. Virus-host prediction revealed that Actinomycetia dominated bacterial hosts of both ARG- and VFG-carrying viruses, with some VFG-carrying viruses linked to potential human pathogens, e.g., Escherichia albertii and Klebsiella pneumoniae. Co-occurrence network analysis indicated that these disturbances strengthened connections between bacteria, viruses, and ARGs (or VFGs). Our study provides a comprehensive profile of viromes and associated risks in agricultural soil under three disturbances, highlighting the role of viruses in spread of antibiotic resistance and pathogenic risks in agricultural soil.}, } @article {pmid40749656, year = {2025}, author = {Asghar, MU and Zhai, Y and Liu, T and Fan, P and Ain, NU and Zaidi, AH and Tariq, M and Mainar-Jaime, RC and Jeong, KC}, title = {A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139384}, doi = {10.1016/j.jhazmat.2025.139384}, pmid = {40749656}, issn = {1873-3336}, mesh = {Pakistan ; *Metagenomics ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Humans ; Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/transmission ; Microbiota ; }, abstract = {Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.}, } @article {pmid40712359, year = {2025}, author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y}, title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139327}, doi = {10.1016/j.jhazmat.2025.139327}, pmid = {40712359}, issn = {1873-3336}, mesh = {*Archaea/drug effects/genetics ; *Microplastics/toxicity ; *Bacteria/drug effects/genetics ; *Water Pollutants, Chemical/toxicity ; *Rivers/microbiology ; Biodegradation, Environmental ; Polyvinyl Chloride/toxicity ; Microbiota/drug effects ; Polyesters ; Drug Resistance, Microbial/genetics ; }, abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.}, } @article {pmid40706155, year = {2025}, author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG}, title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139281}, doi = {10.1016/j.jhazmat.2025.139281}, pmid = {40706155}, issn = {1873-3336}, mesh = {Animals ; *Gene Transfer, Horizontal ; Swine ; *Gastrointestinal Microbiome/genetics ; *Plasmids/genetics ; Humans ; Farms ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.}, } @article {pmid40682875, year = {2025}, author = {Beltrán de Heredia, I and Sbaffi, T and González-Gaya, B and Di Cesare, A and Sabatino, R and Alkorta, I and Ruiz-Romera, E}, title = {Comparative analysis of planktonic and sessile microbiomes and associated resistomes in a freshwater ecosystem impacted by municipal wastewater treatment plant discharge.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139250}, doi = {10.1016/j.jhazmat.2025.139250}, pmid = {40682875}, issn = {1873-3336}, mesh = {*Microbiota/drug effects ; *Wastewater ; Biofilms ; *Plankton/drug effects ; *Fresh Water/microbiology ; Rivers/microbiology ; Ecosystem ; Waste Disposal, Fluid ; Water Microbiology ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical ; }, abstract = {Wastewater treatment plants (WWTPs) disrupt freshwater ecosystems and are recognised as hotspots for antimicrobial resistance. This study assessed the effect of treated municipal wastewater discharge on both planktonic and sessile freshwater microbial communities. A monitoring network was established in a Spanish urban river basin during 2022 dry season, with sampling points upstream and downstream of a WWTP. Artificial glass-based substrates enabled biofilm colonisation, while river water and effluent samples were collected during biofilm harvesting. Chemical exposure was assessed by characterising nutrients and antimicrobial concentrations in water, while shotgun metagenomics revealed taxonomic composition and resistome pools in both matrices. River water exhibited greater genus richness and pathobiome diversity than biofilms. Wastewater discharge shaped microbial composition, leading to shifts in less dominant groups, with partial attenuation of this effect downstream. Resistome richness was higher in river water compared to biofilm, though the latter displayed greater total abundances and distinct resistance profiles suggesting their role as genetic reservoirs. While no consistent resistome trends were linked to sampling location, higher total resistance abundances occurred in river water at sites impacted by wastewaters. Background resistance levels found upstream likely persisted downstream due to pollutant-driven selection. Lower resistome richness in effluent water suggests downstream abundances may also result from microbiome shifts and environmental factors. Assembly-based analysis revealed resistance genetic contexts and indicators of gene dissemination.}, } @article {pmid40645301, year = {2025}, author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C}, title = {Alcohol, aging, and the gut microbiome: Intersections of immunity, barrier dysfunction, and disease.}, journal = {Alcohol (Fayetteville, N.Y.)}, volume = {128}, number = {}, pages = {1-12}, doi = {10.1016/j.alcohol.2025.07.001}, pmid = {40645301}, issn = {1873-6823}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology/physiology ; *Aging/immunology ; *Alcohol Drinking/immunology/adverse effects ; Intestinal Mucosa/drug effects/immunology ; *Ethanol/adverse effects ; Animals ; Inflammation ; }, abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2∗2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.}, } @article {pmid40643197, year = {2025}, author = {Xu, T and Wu, X and Zhang, Y and Cai, Y and Zhang, X and Zeng, Q and Luo, J and Wei, J and Chen, T}, title = {L-Tryptophan Produced by Bifidobacterium pseudocatenulatum NCU-08 Delays Aging in SAMP8 Mice by Activating the Sirt1/P53/P21/Rb Signaling Pathway.}, journal = {Aging cell}, volume = {24}, number = {9}, pages = {e70166}, doi = {10.1111/acel.70166}, pmid = {40643197}, issn = {1474-9726}, support = {32201250//National Natural Science Foundation of China/ ; 2024YFA1307103//National Key R&D Program of China/ ; 2024SSY07061//Jiangxi Province Key Laboratory of bioengineering drugs/ ; 20242BAB25464//Jiangxi Provincial Natural Science Foundation/ ; }, mesh = {Animals ; Mice ; *Sirtuin 1/metabolism ; *Tryptophan/pharmacology/biosynthesis/metabolism ; *Signal Transduction/drug effects ; *Aging/drug effects ; *Bifidobacterium/metabolism ; *Tumor Suppressor Protein p53/metabolism ; Probiotics/pharmacology ; Male ; Gastrointestinal Microbiome ; Hippocampus ; }, abstract = {Gut microbiota delays aging by regulating the immune, metabolic, and neurological functions of the host. However, current research on novel probiotics with antiaging properties significantly lags, impacting their application in clinical treatments. In this study, metagenomics, culturomics, and probiotic property screening were used to identify Bifidobacterium pseudocatenulatum NCU-08 as a potential probiotic with anti-aging properties. In addition, B. pseudocatenulatum NCU-08 effectively improved the behavioral characteristics, significantly reduced the levels of the age-related protein β-galactosidase (β-gal) (BP: M = 0.81 vs. 1.13, p < 0.05), attenuated neuronal damage in the hippocampus, and improved the composition of the gut microbiota of senescence-accelerated mouse tendency-8 (SAMP8) mice. The targeted metabolomics suggested that L-tryptophan (L-Trp) may be a key substance for B. pseudocatenulatum NCU-08 to exert anti-aging effects (BP: M = 14878.6 ng/mL vs. 5464.99 ng/mL, p < 0.01). Mechanistically, using the aging model of SAMP8 mice and HT22 mouse hippocampal neuronal cells, it was found that B. pseudocatenulatum NCU-08 might enter the intestine to regulate L-Trp, and then transport it to the brain. In the brain, L-Trp was metabolized to NAD[+], which activated the Sirt1/P53/P21/Rb signaling pathway, thereby exerting antiaging effects. Interestingly, this antiaging effect was inhibited after the intervention of the Sirt1 inhibitor EX-527. This study is the first to confirm the antiaging properties of NCU-08 isolated from the fecal samples of seven centenarians in Jiangxi Province, providing data support for the future development of probiotic preparations with antiaging effects.}, } @article {pmid40461059, year = {2025}, author = {Laiola, M and Koppe, L and Larabi, A and Thirion, F and Lange, C and Quinquis, B and David, A and Le Chatelier, E and Benoit, B and Sequino, G and Chanon, S and Vieille-Marchiset, A and Herpe, YE and Alvarez, JC and Glorieux, G and Krukowski, H and Huys, GR and Raes, J and Fouque, D and Massy, ZA and Ehrlich, SD and Stengel, B and Wagner, S and , }, title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.}, journal = {Gut}, volume = {74}, number = {10}, pages = {1624-1637}, doi = {10.1136/gutjnl-2024-334634}, pmid = {40461059}, issn = {1468-3288}, mesh = {*Renal Insufficiency, Chronic/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Disease Progression ; Male ; Female ; Middle Aged ; Animals ; Mice ; Fecal Microbiota Transplantation ; Longitudinal Studies ; *Uremic Toxins/metabolism/blood ; Aged ; Metagenomics ; Adult ; Diet ; }, abstract = {BACKGROUND: The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.

OBJECTIVE: To characterise relationships between gut microbiome composition and functionality, UTs diet, and CKD severity and progression, as well as assess microbial contributions to UTs accumulation through mice faecal microbiota transplantation (FMT).

DESIGN: This study profiled the gut microbiome of 240 non-dialysis patients with CKD (CKD-REIN cohort) using shotgun metagenomics, with follow-up in 103 patients after 3 years, with comparisons with healthy volunteers from the Milieu Intérieur cohort. A multiomics approach identifies features associated with CKD severity (and progression), with validation in an independent Belgian cohort. Experimental models used FMT to test CKD gut microbiome effects on UTs and kidney fibrosis. Changes in gut microbiome over time were evaluated, and the impact of diet on these changes was assessed.

RESULTS: Compared with matched healthy controls, patients with CKD exhibited gut microbiota alteration, with enrichment of UT precursor-producing species. Patients with severe CKD exhibited higher UT levels and greater enrichment of UT (precursor)-producing species in the microbiota than patients with moderate CKD. Over time, UT (precursor)-producing species increased, and a plant-based low protein diet appeared to mitigate these changes. FMT from patients with CKD to antibiotic-treated CKD model mice increased serum UT levels and exacerbated kidney fibrosis.

CONCLUSIONS: This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.}, } @article {pmid40918253, year = {2025}, author = {McMahon, S and Franklin, S and Galloway-Peña, J}, title = {Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1629422}, pmid = {40918253}, issn = {2235-2988}, mesh = {Humans ; *Machine Learning ; *Leukemia, Myeloid, Acute/drug therapy/microbiology/complications ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Induction Chemotherapy/adverse effects ; Bacteria/drug effects/genetics/classification ; Aged ; Adult ; Feces/microbiology ; Metagenomics ; *Drug Resistance, Bacterial ; }, abstract = {INTRODUCTION: Acute myeloid leukemia (AML) patients are highly susceptible to infection. Moreover, prophylactic and empirical antibiotic treatment during chemotherapy disrupts the gut microbiome, raising the risk for antibiotic-resistant (AR) opportunistic pathogens. There is limited data on risk factors for AR infections or colonization events in treated cancer patients, and no predictive models exist. This study aims to combine metagenomic and antibiotic administration data to develop a model predicting AR event outcomes.

METHODS: Baseline stool microbiome, antibiotic administration, resistome, and clinical metadata from 95 patients were utilized to build a Random Forest model to predict AR infection and colonization events by serious AR threats. Additionally, sparse canonical correlation analysis assessed correlations between microbiome and resistome data, while Spearman correlation networks identified direct associations with AR event outcomes and secondary variables.

RESULTS: AR-events were identified in 14 of the 95 included patients, with 8 developing AR infections and 9 identified as AR colonized. A Random Forest model predicted AR event outcomes (AUC = 0.73), identifying bacterial taxa and antibiotic resistance gene (ARG) classes as key variables of importance. Methanobrevibacter smithii, Clostridium leptum, and Bacteroides dorei were identified as key taxa associated with reduced risk of AR events, suggesting the potential roles of commensals in maintaining gut microbial resilience during chemotherapy. ARG classes, particularly those conferring resistance to lincosamides, macrolides, and streptogramins, were negatively associated with AR events.

CONCLUSION: These results underscore the value of integrating microbiome and resistome features to reveal potential protective mechanisms and improve risk prediction for AR outcomes in vulnerable patients.}, } @article {pmid40914968, year = {2025}, author = {Cho, Y and Kim, E and Kim, M and Rho, M}, title = {DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {5}, pages = {}, pmid = {40914968}, issn = {1477-4054}, support = {RS-2023-00217123//MSIT/ ; RS-2023-KH135226//Ministry of Health/ ; 2023ER210902/GF/NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; *Interspersed Repetitive Sequences ; Metagenome ; Metagenomics/methods ; Humans ; Neural Networks, Computer ; Sequence Analysis, DNA ; Drug Resistance, Microbial/genetics ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {MOTIVATION: Mobile genetic elements (MGEs) play an important role in facilitating the acquisition of antibiotic resistance genes (ARGs) within microbial communities, significantly impacting the evolution of antibiotic resistance. Understanding the mechanism and trajectory of ARG acquisition requires a comprehensive analysis of the ARG-carrying mobilome-a collective set of MGEs carrying ARGs. However, identifying the mobilome within complex microbiomes poses considerable challenges. Existing MGE prediction methods, designed primarily for single genomes, exhibit substantial limitations when applied to metagenomic data, often producing high false positive rates in identifying target MGEs from metagenome sequencing data.

RESULTS: To address these challenges, we developed DeepMobilome, a novel approach for accurately identifying target MGEs within the microbiome. DeepMobilome leverages a convolutional neural network trained on read alignment data derived from sequence alignment map (SAM) files, providing superior accuracy in detecting MGEs. Trained on 364 647 cases, DeepMobilome achieved a high validation accuracy of 0.99. DeepMobilome consistently outperformed existing methods in discerning the presence of target MGE sequences across diverse test sets. In single-genome test scenarios, DeepMobilome showed an F1-score of 0.935, compared to 0.755 and 0.670 for MGEfinder and ISMapper, respectively, demonstrating its substantial improvements in prediction accuracy. Extensive evaluations across simulated microbiomes further validated the robustness and reliability of DeepMobilome in practical applications. In real microbiome data, DeepMobilome successfully identified six ARG-carrying MGEs across diverse populations. By addressing the limitations of current methods, DeepMobilome offers a powerful tool for advancing our understanding of ARG dissemination and supports targeted interventions in combating antibiotic resistance.}, } @article {pmid40780374, year = {2025}, author = {Mao, Z and Liu, C and Ni, J and Huang, M and Qu, W and Chen, W and Shen, Y and Qin, T and Gao, M and Zheng, S and Chen, Y}, title = {Gut derived (S)-Equol mitigates influenza viral pneumonia by modulating macrophage polarization via Nrf2 mediated AKT/ERK/NF-κb signaling pathways.}, journal = {Free radical biology & medicine}, volume = {239}, number = {}, pages = {457-471}, doi = {10.1016/j.freeradbiomed.2025.08.004}, pmid = {40780374}, issn = {1873-4596}, mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; NF-kappa B/metabolism/genetics ; Proto-Oncogene Proteins c-akt/metabolism/genetics ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/immunology/metabolism ; Signal Transduction/drug effects ; Humans ; *Pneumonia, Viral/drug therapy/pathology/metabolism/virology/immunology ; *Orthomyxoviridae Infections/drug therapy/virology/pathology ; *Influenza, Human/virology/drug therapy ; Male ; Influenza A virus/pathogenicity ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; }, abstract = {Respiratory virus including influenza A virus (IAV) infection induces alterations in gut microbiota structure and function, which in turn plays an essential role in the pathogenic process. Alterations in gut microbiota are usually accompanied with changes in metabolites. The specific relationship between dynamic changes in gut microbiota and serum metabolites in influenza remains unclear. In this study, we depicted dynamic changes in composition of gut microbiota by using metagenomic sequencing in an influenza mouse model. Through mass spectrometry based metabolomic, we identified (S)-Equol as a notable protective metabolite derived from intestinal flora. Serum (S)-Equol level decreased from the initial infection phase and increased gradually during the convalescence phase, which was positively associated with the changes in some Eggerthella and Bifidobacterium species. Antibiotic treatment reduced serum (S)-Equol level and exacerbated lung pathological damage. Oral administration of (S)-Equol relieved disease severity and controlled inflammatory infiltration. Mechanistically, (S)-Equol activated Nrf2 in macrophages, thereby inhibited AKT, ERK and NF-κB phosphorylation. The inhibition of these signaling pathways ultimately restrained pro-inflammatory cytokines release and repressed pro-inflammatory macrophage polarization. Moreover, serum (S)-Equol level was lower in influenza patients at progressed phase and was negatively correlated with serum levels of IL-6, IL-1β, and TNF-α. Collectively, our data highlighted gut derived (S)-Equol a promising postbiotic for alleviating influenza pneumonia.}, } @article {pmid40773868, year = {2025}, author = {Kim, SY and Woo, SY and Kim, HR and Kim, NY and Kim, HL and Chang, Y and Ryu, S and Kim, HN}, title = {Shotgun metagenomics reveals alteration of gut microbiota and metabolic pathways in adults with poor sleep quality.}, journal = {Psychoneuroendocrinology}, volume = {180}, number = {}, pages = {107565}, doi = {10.1016/j.psyneuen.2025.107565}, pmid = {40773868}, issn = {1873-3360}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; Adult ; Middle Aged ; *Metabolic Networks and Pathways/genetics/physiology ; Feces/microbiology ; Metagenomics/methods ; *Sleep Quality ; *Sleep Wake Disorders/microbiology/metabolism ; Metagenome/genetics ; }, abstract = {INTRODUCTION: Emerging evidence suggests that the gut microbiome plays a role in sleep disturbance. This study explored the characteristics of the gut microbiome and the functional metabolic pathways related to sleep quality.

METHODS: A total of 588 participants were recruited. Sleep quality was assessed using the Pittsburgh Sleep Quality Index, employing a cutoff score of 8.5. Based on this criterion, 42 individuals with poor sleep quality (PSQ) and 546 healthy controls with good sleep quality (GSQ) were identified. The fecal microbiome was analyzed using shotgun whole-metagenome sequencing, and groups were compared based on diversity metrics, differentially abundant species, metabolic pathways and metabolites.

RESULTS: No significant differences in alpha and beta diversity indices were observed between individuals experiencing subjective sleep disturbances and those who did not. Klebsiella pneumoniae was more abundant in the PSQ group (β = 0.476; q = 0.017). Additionally, the following metabolic pathways were enriched in the PSQ group: octane oxidation (coefficient = 0.495, q = 0.033), the superpathway of acetyl-CoA biosynthesis (coefficient = 0.377, q = 0.025), superpathway of (Kdo)2-lipid A biosynthesis (coefficient = 0.367, q = 0.026), petroselinate biosynthesis (coefficient = 0.353, q = 0.034), and superpathway of histidine, purine, and pyrimidine biosynthesis (coefficient = 0.349, q = 0.042). When metabolites levels associated with poor sleep quality were inferred using MelonnPan, higher xanthine levels were observed in the PSQ group (coefficient = 0.018; q = 0.025).

CONCLUSION: In summary, this study poses significant questions regarding the relationship between the gut microbiome and poor sleep quality.}, } @article {pmid40719338, year = {2025}, author = {Louca, S and Mullin, CE}, title = {Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e70020}, doi = {10.1111/1755-0998.70020}, pmid = {40719338}, issn = {1755-0998}, support = {2243038//US National Science Foundation/ ; }, mesh = {*Desiccation/methods ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Specimen Handling/methods ; Vacuum ; Feces/microbiology ; Hot Temperature ; Metagenomics/methods ; Soil Microbiology ; }, abstract = {Sample preservation in the field and during transport can be a logistical challenge for microbiome surveys, particularly in remote areas. Sample desiccation eliminates the need for complicated cold chains and dangerous preservatives. However, the effects of desiccation on modern microbiome workflows such as gene-centric metagenomic profiling and metagenome-assembled genome (MAG) binning, remain poorly understood. In addition, most common desiccation tools such as lyophilisation cannot easily be deployed in the field. Here, we describe a proof-of-principle sample desiccator using vacuum and heat, specifically built for deployment in the field and exhibiting low power consumption and cost. We then test the effects of vacuum-heat-assisted sample desiccation followed by storage at room temperature, in comparison to conventional freezing, on multiple soil and animal faecal samples, via metagenomic and 16S rRNA amplicon sequencing. We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG construction, as well as effects on inferred microbial community composition. We find that the impact of drying on considered success metrics was almost always either minor, non-significant or positive. For a subset of source materials we observed moderate but statistically significant differences in terms of inferred microbial taxonomic and genetic composition. We conclude that vacuum- and heat-assisted desiccation can be a useful, practical and cost-effective tool for microbiome field surveys, when a high consistency with frozen samples is not required.}, } @article {pmid40671648, year = {2025}, author = {Maiello, G and Lippert, MR and Neave, EF and Hanson, EA and Palumbi, SR and Mariani, S}, title = {Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e70010}, doi = {10.1111/1755-0998.70010}, pmid = {40671648}, issn = {1755-0998}, support = {//The Pew Charitable Trusts under the Lenfest Ocean Program/ ; //The Gordon and Betty Moore Foundation/ ; //Oceankind Labs/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Kelp ; Ecosystem ; California ; Animals ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Biota ; }, abstract = {The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.}, } @article {pmid40644733, year = {2025}, author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H}, title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.}, journal = {Archives of oral biology}, volume = {178}, number = {}, pages = {106347}, doi = {10.1016/j.archoralbio.2025.106347}, pmid = {40644733}, issn = {1879-1506}, mesh = {Humans ; *Military Personnel ; *Saliva/microbiology ; *Microbiota ; Male ; Adult ; Phylogeny ; *Mouth/microbiology ; Young Adult ; Bacteria/classification ; Metagenomics ; }, abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.

DESIGN: We collected saliva samples from 10 soldiers with good oral health and hygiene habits before and after training. Subsequently, DNA extraction, metagenomic sequencing, and phylogenetic analysis of the oral microbiome were conducted.

RESULTS: 7733 bacterial species from 113 known bacterial phyla and 2017 genera detected in 20 samples. The diversity and richness of saliva microorganisms before and after training were similar (p > 0.05), while beta diversity analysis showed structural differences in microbiota at the phylum and genus levels (p < 0.05). The relative abundance of 27 genera such as Proteobacteria, Neisseria, Morococcus cerebrosus and Eikenella in soldiers' saliva significantly increased after high-intensity training (p < 0.05). Conversely, the relative abundance of 20 genera such as Bacteroidota, Veillonella, Parvimonas micra, Prevotella oris, Peptostreptococcus, and Treponema decreased (p < 0.05). At the metabolic level, training resulted in a relative increase (p < 0.05) in various pathways, including amino acid metabolism, sulfur metabolism, glutathione metabolism, and Tyrosine metabolism. By comparison, after training, carbohydrate metabolism, glycan biosynthesis, metabolism, the HIF-1 signaling pathway, and necroptosis revealed a relative decrease (p < 0.05).

CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.}, } @article {pmid40577531, year = {2025}, author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS}, title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf126}, pmid = {40577531}, issn = {1751-7370}, support = {GBMF9200//Gordon and Betty Moore Foundation/ ; 1394//UK NERC NEOF Pilot Genomics Competition/ ; MR/S037195/1//MRC Methodology Grant "Strain resolved metagenomics for medical microbiology"/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme Grant (Decoding Biodiversity)/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme Grant (Decoding Biodiversity)/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; }, mesh = {*Cyanobacteria/metabolism/genetics/classification/growth & development ; *Biodiversity ; Metagenomics ; Gene Expression Profiling ; Oxygen/metabolism ; }, abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via metatranscriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.}, } @article {pmid40499635, year = {2025}, author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F}, title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.}, journal = {Environmental research}, volume = {283}, number = {}, pages = {122108}, doi = {10.1016/j.envres.2025.122108}, pmid = {40499635}, issn = {1096-0953}, mesh = {Animals ; Hong Kong ; Rats/microbiology ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA, as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.}, } @article {pmid40459094, year = {2025}, author = {Dahl, MB and Brachmann, S and Söllinger, A and Schnell, M and Ahlers, L and Wutkowska, M and Hoff, KJ and Nath, N and Groß, V and Wang, H and Weil, M and Piecha, M and Schaffer, M and Jensen, C and Kuss, AW and Gall, C and Wimmer, E and Pribasnig, T and Tveit, AT and Sigurdsson, BD and Schleper, C and Richter, A and Urich, T}, title = {Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques-Cross-Validation and Perspectives.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14130}, doi = {10.1111/1755-0998.14130}, pmid = {40459094}, issn = {1755-0998}, support = {21-17322M//The Czech Science Foundation/ ; BO 5559/1-1//Deutsche Forschungsgemeinschaft/ ; INST 292/146-1 FUGB//Deutsche Forschungsgemeinschaft/ ; UR198/7-1//Deutsche Forschungsgemeinschaft/ ; 813114//HORIZON EUROPE European Innovation Council/ ; //Research Council of Norway/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gene Expression Profiling/methods ; *Bacteria/genetics/classification ; Transcriptome ; Soil/chemistry ; }, abstract = {Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.}, } @article {pmid40243260, year = {2025}, author = {Bayer, PE and Bennett, A and Nester, G and Corrigan, S and Raes, EJ and Cooper, M and Ayad, ME and McVey, P and Kardailsky, A and Pearce, J and Fraser, MW and Goncalves, P and Burnell, S and Rauschert, S}, title = {A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.}, journal = {Molecular ecology resources}, volume = {25}, number = {7}, pages = {e14107}, doi = {10.1111/1755-0998.14107}, pmid = {40243260}, issn = {1755-0998}, support = {//Minderoo Foundation/ ; }, mesh = {Animals ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; *DNA, Environmental/genetics ; Computational Biology/methods ; Australia ; *Metagenomics/methods ; Biodiversity ; RNA, Ribosomal/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.}, } @article {pmid40081359, year = {2025}, author = {Ali, MJ}, title = {Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.}, journal = {Ophthalmic plastic and reconstructive surgery}, volume = {41}, number = {5}, pages = {584-588}, pmid = {40081359}, issn = {1537-2677}, mesh = {Humans ; Prospective Studies ; *Lacrimal Duct Obstruction/congenital/microbiology ; *Metagenomics/methods ; *Nasolacrimal Duct/microbiology ; Male ; Female ; *Bacteria/genetics/isolation & purification ; *Microbiota ; Dacryocystorhinostomy ; *Fungi/genetics/isolation & purification ; Child ; Child, Preschool ; *Metagenome ; Infant ; *Lacrimal Apparatus/microbiology ; }, abstract = {PURPOSE: To study the metagenomics of microbes isolated from the lacrimal sacs of patients with congenital nasolacrimal duct obstruction (CNLDO).

METHODS: A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from the patients with CNLDO who underwent endoscopic dacryocystorhinostomy at a tertiary care dacryology service. Immediately after a full-length lacrimal sac marsupialization, the samples were collected and transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina platform following DNA extraction and library preparation. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in the SqueezeMeta pipeline, and the functional annotation was performed using the MetaCerberus, v1.3.1.

RESULTS: The taxonomic hit distribution across the samples showed that bacteria were the most common isolates, followed by fungi and viruses. The major bacterial phyla identified across the samples of CNLDO were proteobacteria, firmicutes, actinobacteria, and bacteroidetes. The prevalent organisms include Haemophilus influenzae , Streptococcus pneumoniae , Stenotrophomonas maltophilia , Achromobacter xylosoxidans, Staphylococcus aureus , and Ochrobactrum anthropi , among others. The predominant fungal species identified include Botrytis cinerea , Aspergillus oryzae , and Fusarium fujikuroi . Several species of pandoravirus were the common viruses recognized.

CONCLUSIONS: This is the first whole metagenome sequencing of the lacrimal sac contents from patients with CNLDO, which showed that the sacs harbored diverse microbial communities of bacteria, fungi, and viruses. Further work is needed to decipher the polymicrobial interactions and their relationship with CNLDO.}, } @article {pmid40910796, year = {2025}, author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R}, title = {The Earth Hologenome Initiative: Data Release 1.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40910796}, issn = {2047-217X}, support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação/ ; 25925//Villum Fonden/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; }, abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.

RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.

CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.}, } @article {pmid40749888, year = {2025}, author = {Carella, F and Correggia, M and Cordone, A and Iacovino, O and Maresca, F and Villari, G and Roque, A and Vico, G}, title = {Bald disease in a natural population of the purple sea urchin Paracentrotus lividus of the Mediterranean Sea: From spines to tissues.}, journal = {Journal of invertebrate pathology}, volume = {213}, number = {}, pages = {108415}, doi = {10.1016/j.jip.2025.108415}, pmid = {40749888}, issn = {1096-0805}, mesh = {Animals ; *Paracentrotus/microbiology ; Mediterranean Sea ; Microbiota ; }, abstract = {Recently, unusual mortality outbreaks have been reported in the echinoderm populations over broad geographic regions. The present work used different diagnostic approaches to unravel the Bald Sea Urchin Disease (BSUD) causes in a natural population of Paracentrotus lividus from the Gulf of Naples sampled in 2021. Symptomatic individuals displayed the typical signs such as test discoloration and ulceration, loss of spines and pedicellariae and visceral hyperpigmentation. Scanning electron microscopy of diseased individuals (stage 2 and stage 3) revealed a bare exoskeleton with multiplying bacteria penetrating the damaged test, and histopathology revealed inflammatory lesions and phagocytosis only in stages 2 and 3, with Gram negative and positive bacteria at stage 3. Metagenomics revealed an increase in DNA virus and Proteobacteria during disease progression. Microbial community analyses failed to reveal a single putative pathogen associated with symptoms, but microbiome analysis showed higher diversity in asymptomatic individuals compared to the symptomatic. Different Vibrio spp. belonging to the Splendidus clade were also isolated, with V. crassostreae as the most represented in advanced stages of disease. We cannot confirm that the observed microorganisms were associated with tissue damage and their contribution to the disease outcome remains unclear as they could be just opportunistic in the lesions. This preliminary study on a wild population highlights the importance of morphological analysis (histopathology and SEM) coupled with microbiome and metagenome analyses in sea urchin disease investigations. Moreover, we suggest also performing transmission electron microscopy (TEM), experimental challenges and in situ hybridization methods (ISH) to provide morphological evidence of potential infective agents. Future studies should also include histopathology of the test.}, } @article {pmid40909338, year = {2025}, author = {Borgognone, A and Prats, A and Sharma, AA and Martinez-Zalacaín, I and Soriano-Mas, C and Brander, C and Clotet, B and Moltó, J and Mothe, B and Sekaly, RP and Paredes, R and Muñoz-Moreno, JA}, title = {Interactions between gut microbiota, plasma metabolome and brain function in the setting of a HIV cure trial.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1629901}, pmid = {40909338}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *HIV Infections/drug therapy/complications/microbiology ; Male ; Female ; *Brain/physiopathology/physiology ; Adult ; Biomarkers/blood ; Middle Aged ; Feces/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; HIV-1/drug effects ; }, abstract = {BACKGROUND: The intestinal microbiota composition has been linked to neurocognitive impairment in people with HIV (PWH). However, the potential interplay of microbial species and related metabolites, particularly in the context of an HIV cure strategy remains underexplored. The BCN02 trial evaluated the impact of romidepsin (RMD), used as a HIV-1 latency reversing agent and with reported beneficial neurological effects, combined with the MVA.HIVconsv vaccine on virus control during 32-weeks of monitored antiretroviral treatment interruption (MAP) in early-treated HIV-infected individuals. Here, we analyzed longitudinal gut microbiome, plasma metabolome and brain functioning data to identify potential associations and novel putative biomarkers of HIV-associated neurocognitive disorders (HAND).

METHODS: Data from fecal shotgun metagenomics, plasma metabolome, cognitive (standardized neuropsychological test score covering 6 cognitive domains, NPZ-6), functional (neuropsychiatric symptoms) and neuroimaging assessments were obtained and evaluated in 18 participants before and after RMD administration, and at the study end (post-MAP follow-up) in the BCN02 trial.

RESULTS: Participants with neurocognitive impairment (Lower vs. Higher NPZ-6 score group) were enriched in bacterial species, including Desulfovibrio desulfuricans, Sutterella wadsworthensis and Streptococcus thermophilus, and showed higher 1,2-propanediol degradation microbial pathway levels, before RMD administration. A multi-omics profiling showed significant and positive correlations between these microbial features and lipid-related metabolic pathways, previously linked to neurological disorders (i.e., sphingolipid, ether lipid, and glycerophospholipid metabolism), in participants with neurocognitive impairment, before RMD administration. Three indices (microbial-, metabolite-based and combined) obtained from the discriminant features were assessed longitudinally, showing progressive similarities between NPZ-6 score groups over time. Furthermore, the three indices and related discriminant features correlated negatively with functional outcomes, such as quality of life and daily functioning, and positively with depression, stress and CNS-related symptoms before RMD administration, while these associations became less discernible at the subsequent timepoints.

CONCLUSIONS: While the direct effect of the intervention on the observed shifts cannot be conclusively determined in this study settings, these findings strengthen the link between gut bacteria, related metabolites, and neurocognitive function in PWH, and provide an analytical framework for future validation studies aimed at discovering predictive biomarkers for neurocognitive impairment in PWH.}, } @article {pmid40908554, year = {2025}, author = {Susilowati, A and Christita, M and Larekeng, SH and Lateef, AA and Ren, W and Azeez, AA and Simarmata, R and Khairina, Y and Khumairah, FH and Elfiati, D and Asiegbu, FO}, title = {Forest Type, Bark Wounding, and Tapping: Their Combined Influence on Bacteria Biota of Styrax Paralleloneurus in Natural and Community Forest.}, journal = {Environmental microbiology reports}, volume = {17}, number = {5}, pages = {e70184}, doi = {10.1111/1758-2229.70184}, pmid = {40908554}, issn = {1758-2229}, support = {353365//Research Council of Finland/ ; 13/UN5.2.3.1/PPM/KP-WCU/2022//Universitas Sumatera Utara/ ; }, mesh = {*Forests ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Plant Bark/microbiology ; Biodiversity ; Indonesia ; Phylogeny ; *Trees/microbiology ; DNA, Bacterial/genetics ; *Biota ; }, abstract = {Styrax paralleloneurus is a resin-producing tree native to Sumatra, Indonesia. This study investigated the effects of tapping, bark wounding and forest type on bacterial biota in the stem of styrax in natural and community forests. Amplicon metagenomic sequencing of the 16S rRNA region was deployed to identify the bacterial communities associated with tapped and untapped trees across various environmental and experimental conditions. The results of the study showed that tapped trees had lower abundance and diversity of Pseudomonas compared to untapped trees, largely due to their increased exposure to external microbe communities and environmental elements. Serratia and Pantoea were more abundant in natural forest than community forest, while Bradyrhizobium lablabi was found abundantly in untapped trees. Additionally, the taxonomic analysis revealed distinct responses of bacterial genera to tapping and forest type, indicating that community forests could play a significant role in promoting biodiversity in forest ecosystems. This finding underscores the importance of community forests in biodiversity conservation. These insights can inform future conservation and management strategies to enhance biodiversity and underscore the need for sustainable forest management practices to maintain forest health and productivity.}, } @article {pmid40816430, year = {2025}, author = {Kong, Z and Wang, H and Man, S and Yan, Q}, title = {Magnetite modulates bacterial cooperation during cathodic nitrogen removal in bioelectrochemical systems under trace dissolved oxygen.}, journal = {Bioresource technology}, volume = {437}, number = {}, pages = {133147}, doi = {10.1016/j.biortech.2025.133147}, pmid = {40816430}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources/microbiology ; *Denitrification/drug effects ; Electrodes ; *Ferrosoferric Oxide/pharmacology ; Oxygen ; *Water Purification/methods ; Metagenome ; Ammonium Compounds/metabolism ; *Microbiota ; }, abstract = {Nitrate and ammonium co-contamination poses a major challenge for sustainable nitrogen removal, especially under microoxic conditions. This study investigated the effect of magnetite on microbial nitrogen metabolism and nitrite accumulation in biocathodes of bioelectrochemical systems under 0.25 mg/L dissolved oxygen. Magnetite improved total nitrogen removal by 22.8 %, reduced peak nitrite levels by 22.6 %, and lowered residual ammonium by 49.2 %. Magnetite promoted interspecies cooperation, driving modular specialization in nitrite reduction while suppressing dissimilatory nitrate reduction to ammonium. Concurrently, it stimulated ammonia-oxidizing bacteria activity, accelerating ammonium conversion and mitigating nitrite accumulation through enhanced denitrification. A cooperative microbial pattern emerged, with dominant species such as Hanamia sp. and Moheibacter sp. carrying out nitrite reduction, while less abundant species performed single nitrogen metabolic processes. This study highlights the role of magnetite in integrating aerobic and anaerobic nitrogen pathways, offering a sustainable strategy for controlling complex nitrogen pollution.}, } @article {pmid40763378, year = {2025}, author = {Mollick, SA}, title = {Genetic sex prediction from human gut shotgun metagenomic data: An ethical appraisal.}, journal = {Forensic science international}, volume = {376}, number = {}, pages = {112585}, doi = {10.1016/j.forsciint.2025.112585}, pmid = {40763378}, issn = {1872-6283}, mesh = {Humans ; Male ; Female ; *Metagenomics ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; *Metagenome ; Sequence Analysis, DNA ; Chromosomes, Human, Y ; High-Throughput Nucleotide Sequencing ; Forensic Genetics ; }, abstract = {Human DNA inadvertently captured during gut shotgun metagenomic sequencing is typically treated as background contamination, yet it can reveal sensitive personal traits, raising ethical and forensic concerns. In this study, fecal metagenomes from 626 individuals were processed using four DNA extraction protocols and both paired and single-end sequencing, to evaluate the extent of identifiable human information. Host-derived reads exhibited uniform chromosomal coverage, enabling the accurate prediction of genetic sex based on the Y-to-X read-depth ratio. A machine learning model trained on this metric achieved over 92 % accuracy with the detection threshold (-β0/β1) = 0.34 across different protocols and sequencing configurations, demonstrating the method's robustness and general applicability. These findings highlight that even low levels of residual human DNA in microbiome datasets are sufficient to infer individual traits, such as sex, which can compromise participant anonymity. Given that such reads are often retained in public repositories, the risk of re-identification persists despite microbiome-focused study designs. This work serves as both a technical demonstration and an ethical imperative. Host-DNA masking should become standard before data sharing; ethics boards and data custodians must recognize the potential for unintentional disclosure; and informed consent procedures must reflect the realities of high-throughput sequencing. While the Y-to-X depth ratio offers a scalable quality control and forensic tool, its application must be balanced with rigorous privacy safeguards to uphold research integrity and participant trust.}, } @article {pmid40738886, year = {2025}, author = {Wang, S and Zhang, Z and Zhao, J and Yang, K and Zhang, W and Wang, Z and Liang, Z and Zhang, Y and Zhang, Y and Liu, J and Zhang, L}, title = {Metaproteomic Insights into Bioenergy Conversion Enzymes of Bathypelagic Microbial Communities in the South China Sea.}, journal = {Journal of proteome research}, volume = {24}, number = {9}, pages = {4780-4791}, doi = {10.1021/acs.jproteome.5c00551}, pmid = {40738886}, issn = {1535-3907}, mesh = {China ; *Proteomics/methods ; *Seawater/microbiology ; *Microbiota ; Energy Metabolism ; Metagenomics ; Metagenome ; Archaea/enzymology/genetics ; Oceans and Seas ; Bacteria/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Carbon Cycle ; }, abstract = {Marine microorganisms inhabiting the bathypelagic zone (1000-4000 m) exhibit distinctive environmental adaptability and serve as a valuable reservoir of bioenzymes. However, a limited understanding of deep-sea microbial community composition and metabolic activities hinders the broad application of their enzymatic potential. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities in the bathypelagic layers of the South China Sea (SCS), and we compared them with the corresponding metagenomic data. Our findings revealed a strong phylum-level correlation between metaproteomic and metagenomic datasets, along with a significant enrichment of proteins associated with inorganic ion metabolism and energy conversion. Deep-sea microbial communities are characterized by unique dominant taxa, such as Propionibacteriales, and exhibit diverse strategies for energy utilization. Notably, we identified several enzymes involved in energy conversion, including RuBisCO and carbon monoxide dehydrogenase in Proteobacteria and ammonia monooxygenase in Thaumarchaeota for carbon fixation. These enzymes catalyze reactions utilizing various inorganic substrates as energy sources. Additionally, the deep-sea environment significantly enhanced the expression of methane monooxygenase in methylotrophs, suggesting that such conditions may promote the development of methane-utilizing cell factories. This study not only deepens our understanding of energy conversion mechanisms in deep-sea microorganisms but also offers valuable enzymatic resources for the development of novel bioenergy technologies.}, } @article {pmid40738384, year = {2025}, author = {Liang, T and Jiang, T and Liang, Z and Chen, Y and Chen, T and Dong, B and Xie, X and Gu, B and Wu, Q}, title = {Lactiplantibacillus plantarum strain 84-3-derived l-glutamine ameliorates glucose homeostasis via AMPK/PPARγ signaling pathway activation in type 2 diabetes.}, journal = {Metabolism: clinical and experimental}, volume = {172}, number = {}, pages = {156357}, doi = {10.1016/j.metabol.2025.156357}, pmid = {40738384}, issn = {1532-8600}, mesh = {*Glutamine/metabolism/pharmacology ; *Diabetes Mellitus, Type 2/metabolism ; Animals ; Rats ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Humans ; Male ; *AMP-Activated Protein Kinases/metabolism ; Case-Control Studies ; *PPAR gamma/metabolism ; *Lactobacillus plantarum/metabolism ; *Glucose/metabolism ; Gastrointestinal Microbiome ; Probiotics ; Diabetes Mellitus, Experimental/metabolism ; Blood Glucose/metabolism ; Rats, Sprague-Dawley ; Middle Aged ; Adult ; Female ; }, abstract = {BACKGROUND: Gut microbiota and their metabolites play an essential role in type 2 diabetes (T2D). However, contributions of individual bacterial strains and their metabolites to T2D pathogenesis remain poorly understood. We investigated T2D regulation by Lactobacillus in various animal models to understand its therapeutic effects.

METHODS AND RESULTS: We performed a case-control study of Chinese adults using metabolome profiling and identified an inverse correlation between l-glutamine and T2D serum concentrations. The glnA and GLUL genes encoding glutamine synthetase (GS) in L. plantarum 84-3 were also identified. L. plantarum 84-3 treatment significantly decreased serum inflammation and improved metabolic phenotypes in streptozotocin- or tetraoxypyrimidine-induced T2D rats, including blood glucose, glucose tolerance, insulin resistance, and lipids. We confirmed elevated serum l-glutamine levels in the L. plantarum 84-3 group. RNA sequencing analysis demonstrated that L. plantarum 84-3-derived l-glutamine is a vital bioactive molecule, improving glucose homeostasis by activating the liver AMPK/PPAR signaling pathway and ameliorating T2D. We conducted co-culture fermentation experiments in vitro and in vivo, and metagenomic and metabolomic analyses revealed that resistance starch combined with L. plantarum 84-3 significantly enriched of Lactobacillus abundance and increased the l-glutamine level, affecting of alanine, aspartate, and glutamate metabolism pathways, which was confirmed in vivo in rats. The reduced L. plantarum and l-glutamine levels were validated in a human T2D cohort.

CONCLUSIONS: These findings revealed a novel therapeutic effect of L. plantarum in alleviating T2D-related glucose homeostasis by increasing circulating l-glutamine, which suggests viable preventive and therapeutic strategies for metabolic disorders.}, } @article {pmid40645526, year = {2025}, author = {Xu, J and Zhang, Y and Wang, X and Xu, W and Chen, S and Pan, L and Gao, J}, title = {A P2X7 receptor antagonist alleviates PTSD-like behaviors in adolescent rats through gut microbiota modulation and hippocampal transcriptomic remodeling.}, journal = {Journal of affective disorders}, volume = {390}, number = {}, pages = {119859}, doi = {10.1016/j.jad.2025.119859}, pmid = {40645526}, issn = {1573-2517}, mesh = {Animals ; *Stress Disorders, Post-Traumatic/drug therapy/microbiology/genetics ; *Gastrointestinal Microbiome/drug effects ; *Hippocampus/drug effects/metabolism ; Rats ; Male ; *Transcriptome/drug effects ; *Purinergic P2X Receptor Antagonists/pharmacology ; Rats, Sprague-Dawley ; Disease Models, Animal ; Behavior, Animal/drug effects ; Receptors, Purinergic P2X7 ; *Rosaniline Dyes/pharmacology ; Dysbiosis/drug therapy ; }, abstract = {Post-traumatic stress disorder (PTSD) is a debilitating psychiatric disorder that frequently manifests during adolescence, a critical neurodevelopmental period. Although the P2X7 receptor is implicated in the pathophysiology of PTSD, its role in adolescent-onset PTSD, particularly concerning gut microbiota dysbiosis and hippocampal transcriptomic alterations, remains unclear. This study investigated the effects of the P2X7 receptor antagonist Brilliant Blue G (BBG) on PTSD-like behaviors, gut microbiota, and hippocampal transcriptomic profiles in adolescent rats subjected to single prolonged stress and electric foot shock (SPS&S). BBG treatment significantly ameliorated SPS&S-induced fear- and anxiety-like behaviors and spatial working memory deficits. Metagenomic analysis revealed that BBG partially reversed SPS&S-induced gut microbiota dysbiosis, significantly enriching key bacterial taxa (e.g., Bacteroidota) and modulating functional pathways related to immunity and metabolism. Hippocampal transcriptomic analysis demonstrated that BBG normalized a majority of SPS&S-induced differentially expressed genes; these corrected genes were significantly enriched in pathways for extracellular matrix organization, neural differentiation, and PI3K-Akt signaling pathway. Integrated multi-omics correlation analyses revealed significant correlations among key microbial abundances, hippocampal gene expression, and behavioral outcomes, supporting a gut-brain axis mechanism underlying the therapeutic effects of BBG. These findings position the P2X7 receptor as a promising therapeutic target for adolescent PTSD and highlight the crucial role of gut microbiota in modulating stress-related neuropathology via the gut-brain axis.}, } @article {pmid40908508, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J}, title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {9}, pages = {e70173}, doi = {10.1111/1462-2920.70173}, pmid = {40908508}, issn = {1462-2920}, support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; }, abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.}, } @article {pmid40904108, year = {2025}, author = {Meaden, S and Westra, ER and Fineran, PC}, title = {Phage defence-system abundances vary across environments and increase with viral density.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1934}, pages = {20240069}, doi = {10.1098/rstb.2024.0069}, pmid = {40904108}, issn = {1471-2970}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //James Cook Research Fellowship (RSNZ, Te Apārangi)/ ; //Philip Leverhulme/ ; //Bioprotection Aotearoa (Tertiary Education Commission, NZ)/ ; //UK Horizon Funding Guarantee/ ; }, mesh = {*Bacteriophages/physiology ; *Bacteria/virology/immunology ; *Microbiota ; *Metagenome ; *Virome ; }, abstract = {The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain unclear, as substantial variation in defence prevalence has been reported. Experimental work in simple communities suggests ecological factors can determine when specific defence systems are most beneficial, but applying these findings to complex communities has been challenging. Here, we use a comprehensive and environmentally balanced collection of metagenomes to survey the defence landscape across complex microbial communities. We also assess the association between the viral community and the prevalence of defence systems. We identify strong environmental effects in predicting overall defence abundance, with animal-host-associated environments and hot environments harbouring more defences overall. We also find a positive correlation between the density and diversity of viruses in the community and the abundance of defence systems. This study provides insights into the ecological factors that influence the composition and distribution of bacterial defence systems in complex microbial environments and outlines future directions for the study of defence-system ecology.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.}, } @article {pmid40856172, year = {2025}, author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, J and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL}, title = {Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.}, journal = {Molecular biology and evolution}, volume = {42}, number = {9}, pages = {}, doi = {10.1093/molbev/msaf202}, pmid = {40856172}, issn = {1537-1719}, mesh = {Animals ; *Geologic Sediments/chemistry ; Humans ; *Bone and Bones/chemistry ; Rats ; *DNA, Ancient/analysis ; Archaeology ; Metagenomics ; Fossils ; Gastrointestinal Microbiome/genetics ; }, abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death.}, } @article {pmid40848630, year = {2025}, author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C}, title = {Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.}, journal = {International journal of food microbiology}, volume = {442}, number = {}, pages = {111399}, doi = {10.1016/j.ijfoodmicro.2025.111399}, pmid = {40848630}, issn = {1879-3460}, mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; *Biogenic Amines/metabolism/analysis ; *Zygosaccharomyces/metabolism ; Temperature ; *Flavoring Agents/metabolism ; Food Microbiology ; Taste ; *Microbial Interactions ; Bacteria/metabolism/genetics/classification/isolation & purification ; Microbiota ; Amino Acids/metabolism ; Odorants/analysis ; Saccharomycetales ; }, abstract = {This study elucidates the temperature-dependent interactions between halotolerant yeasts and microbial communities during secondary fortified soy sauce fermentation (SFFSS) and their implications for flavor enhancement and safety. A dual-mode fermentation system compared natural temperature fermentation (NTF) and controlled temperature fermentation (CTF, 30 °C), each with and without co-inoculation of Zygosaccharomyces rouxii and Wickerhamiella versatilis (ZC). Multi-omics analyses integrating amplicon sequencing, metagenomics, and metabolomics revealed that CTF control elevated amino acid nitrogen and aroma compounds, while increasing biogenic amines (BA) by 47.88 %. In both NTF and CTF modes, the ZC pattern significantly reduced lactic acid while enhancing succinic acid, umami/sweet free amino acids, and key aroma compounds (e.g., 4-ethylguaiacol, 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone), alongside enriching functional bacteria (Staphylococcus, Weissella), stabilizing fungal communities, and suppressing Tetragenococcus and Ligilactobacillus pobuzihii. Mechanistically, ZC pattern promoted tricarboxylic acid cycle flux and amino acid metabolism, synergistically enhancing volatile phenolics, esters, and alcohols, and reduced BA by >87 % via dual modulation of decarboxylase inhibition and oxidase activation. Network analyses linked microbial composition shifts to targeted flavor metabolite synthesis, providing a mechanistic framework for microbial community engineering. These findings highlight yeast-mediated, temperature-driven modulation of microbiota-metabolite networks as a viable strategy for producing high-quality, safe soy sauce with optimized flavor complexity.}, } @article {pmid40840192, year = {2025}, author = {Yang, SB and Lu, ZM and Shen, HJ and Fu, JJ and Yang, Y and Zhang, XJ and Chai, LJ and Wang, ST and Zhang, SY and Shen, CH and Shi, JS and Xu, ZH}, title = {Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.}, journal = {International journal of food microbiology}, volume = {442}, number = {}, pages = {111392}, doi = {10.1016/j.ijfoodmicro.2025.111392}, pmid = {40840192}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; Fermentation ; *Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Bacteria/metabolism/genetics/classification/isolation & purification ; Humans ; Temperature ; Metagenomics ; Metabolic Networks and Pathways ; Edible Grain/microbiology/chemistry ; Taste ; Multiomics ; }, abstract = {Solid-state fermentation heterogeneity causes microenvironmental differences, shaping diverse microbial communities and metabolite compositions. Here, we aimed to investigate the variations in Qu-aroma between the inner (I-) and outer (O-) layers of medium-temperature Daqu (MT-Daqu) starter, and to analyze the differences in microbial communities as well as the associated metabolic pathways related to Qu-aroma volatile organic compounds (VOCs). Firstly, quantitative descriptive analysis revealed that the I-layer exhibited intensified rancid-roasted notes, whereas the O-layer showed stronger grain and woody notes. Secondly, a total of 225 VOCs were identified from 88 inner and outer layer samples using HS-SPME-GC-MS, among which 43 differential VOCs were confirmed between the layers (VIP > 1, P < 0.05, and Fold change ≥1.5 or ≤0.67). Thin film (TF)-SPME-GC-O/MS revealed 52 and 47 odors with corresponding VOCs in the I- and O-layers, respectively. Subsequently, cross-referencing metagenomic and metabolic databases revealed that 37 aroma-active VOCs were functionally linked to six metabolic modules within the MT-Daqu microbial metabolic network. Finally, integrated metagenomic and amplicon sequencing identified potential functional microorganisms associated with specific metabolic modules. Five genera, including Kroppenstedtia and Thermomyces, were identified as characteristic of the I-layer, while 22 genera, such as Lactobacillus and Saccharomycopsis, were characteristic of the O-layer. Notably, Kroppenstedtia, Thermomyces, Lactobacillus, Saccharomycopsis, and Weissella were ubiquitously associated with all six metabolic modules across both layers of MT-Daqu. This study delivers a perspective for clarifying the spatial heterogeneity of Qu-aroma and its microbial drivers.}, } @article {pmid40780971, year = {2025}, author = {Boulanger, N}, title = {Tick and host microbiotas: immunomodulators in tick-borne diseases?.}, journal = {Trends in parasitology}, volume = {41}, number = {9}, pages = {796-805}, doi = {10.1016/j.pt.2025.07.009}, pmid = {40780971}, issn = {1471-5007}, mesh = {Animals ; *Tick-Borne Diseases/microbiology/immunology/prevention & control ; *Microbiota/immunology ; *Ticks/microbiology/immunology ; Humans ; }, abstract = {Vector-borne diseases have a growing impact on human and animal health. Metagenomics has been largely used to characterize the microbiome and has highlighted the key role of the microbiota in modulating the vector competence of insects. Currently, an integrated approach combining vector control, vaccine prevention, and drug treatment is being developed to limit the transmission of insect-borne pathogens. This is more complex for tick-associated diseases, considering the biology of the tick and the possibility of modifications of its microbiota in vector control. Conversely, because the skin is an essential interface in tick-borne diseases, an in-depth study of the precise role of the tick and host microbiota during tick bite and pathogen inoculation opens up new prospects for controlling these diseases.}, } @article {pmid40735808, year = {2025}, author = {Maffei, VJ and Bertoni, AG and Wood, AC and Rotter, JI and Crago, O and Chen, YI and Petrosino, JF and Hoffman, KL and Goodarzi, MO and Jensen, ET}, title = {Menopause factors and alterations in gut microbiota and insulin homeostasis: A cross-sectional analysis of the microbiome and insulin longitudinal evaluation study (MILES).}, journal = {Diabetes, obesity & metabolism}, volume = {27}, number = {10}, pages = {5444-5454}, doi = {10.1111/dom.16578}, pmid = {40735808}, issn = {1463-1326}, support = {P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; 58-3092-5-001//Agricultural Research Service/ ; P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/physiology ; Longitudinal Studies ; Cross-Sectional Studies ; *Insulin Resistance/physiology ; *Menopause/physiology/metabolism ; Homeostasis/physiology ; *Insulin/metabolism/blood ; *Dysbiosis/microbiology/metabolism ; Adult ; Feces/microbiology ; Glucose Tolerance Test ; }, abstract = {AIM: To assess the risk for impaired insulin homeostasis as a function of menopause-related factors and gut microbiota dysbiosis in non-diabetic, post-menopausal women.

MATERIALS AND METHODS: Baseline data (n = 175 women) from the Microbiome and Insulin Longitudinal Evaluation Study (MILES) were used, including insulin and dysglycaemia indices calculated from a 2-h oral glucose tolerance test, untargeted peripheral metabolomics, targeted peripheral short chain fatty-acid levels and faecal bacterial microbiota surveyed by whole-metagenomic sequencing.

RESULTS: After adjustment for covariates, menopause age <50 years and use of hormone replacement therapy (HRT) were associated with lower Matsuda et al. insulin sensitivity index levels (β = -0.232, confidence interval (CI) = [-0.450, -0.014] and β = -0.275, CI = [-0.444, -0.107], respectively) but not pre-menopausal gynaecologic surgery. Pre-menopausal gynaecologic surgery was significantly associated with faecal microbiota beta diversity driven by a relative increase in diabetogenic Ruminococcus gnavus and Clostridium species and a decrease in protective Alistipes species and Akkermansia muciniphila relative abundances. A reduction in two glycerophospholipids in the plasmalogen class significantly statistically mediated an inverse association between gynaecologic surgery before menopause and insulin sensitivity.

CONCLUSIONS: Menopause age and history of HRT are more strongly associated with insulin resistance than gynaecologic surgery before menopause. However, gynaecologic surgery is associated with shifts in gut microbial composition and plasma metabolite levels with a potential to contribute to future diabetes risk.}, } @article {pmid40619005, year = {2025}, author = {Hullar, MA and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW}, title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.}, journal = {The American journal of clinical nutrition}, volume = {122}, number = {3}, pages = {780-792}, doi = {10.1016/j.ajcnut.2025.06.026}, pmid = {40619005}, issn = {1938-3207}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Cross-Over Studies ; Female ; Adult ; *Glycemic Load ; *Diet ; Feces/microbiology ; *Bacteria/classification/genetics/metabolism ; Young Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Dietary patterns characterized by low glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.

OBJECTIVES: Evaluate the effects of a low glycemic load (LGL) compared with a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.

METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n = 69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.

RESULTS: Overall community structure measured by alpha and beta diversity was not significantly different across the diets, although diet did significantly increase the abundance of 13 of 161 genera (Padj < 0.05) and 5 species in the LGL diet and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (β = -1.15; SE = 0.24; 95% confidence interval [CI]: -1.63, -0.67; Padj = 0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (β = 0.20; SE = 0.05; 95% CI: 0.09, 0.30; Padj = 0.03) was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, P < 0.001). CAZymes enriched in the HGL diet reflected dietary additives, whereas CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between homeostasis model assessment of insulin resistance (HOMA-IR) and the coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (Padj = 0.035), which was positive in the HGL diet (b = 0.20; SE = 0.09; 95% CI: 0.02, 0.39) and negative in the LGL diet (β = -0.23; SE = 0.09; 95% CI: -0.40, -0.06).

CONCLUSIONS: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.}, } @article {pmid40600350, year = {2025}, author = {Dike, CR and Duan, Q and Ahmed, F and Denson, LA and Haslam, D and Minar, P and Ollberding, NJ and Papachristou, GI and Setchell, KDR and Thompson, T and Vitale, DS and Zhao, X and Abu-El-Haija, M}, title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {81}, number = {3}, pages = {690-698}, doi = {10.1002/jpn3.70135}, pmid = {40600350}, issn = {1536-4801}, support = {K23DK118190 (MAH)/DK/NIDDK NIH HHS/United States ; R03 DK131156 (MAH)/DK/NIDDK NIH HHS/United States ; P30DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati (LAD) and The Helmsley Charitable Trust (LAD, PM)/ ; K23DK118190/DK/NIDDK NIH HHS/United States ; R03 DK131156/DK/NIDDK NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati; The Helmsley Charitable Trust/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; *Pancreatitis/microbiology/complications ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; Child ; Adolescent ; Feces/microbiology ; Acute Disease ; Child, Preschool ; Recurrence ; Case-Control Studies ; Young Adult ; }, abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP) is associated with gut dysbiosis. We aimed to determine if dysbiosis persisted during follow-up and whether it is associated with clinical outcomes.

METHODS: Prospective enrollment of participants <21 years with first AP. Stool samples were obtained at baseline (n = 41), 3 months (n = 19), and 12 months (n = 12) and in healthy controls (HC; n = 34). Evaluation for diabetes (DM) or prediabetes (pre-DM) was performed. At 12-month follow-up gastrointestinal (GI) symptom surveys were completed and AP recurrence-acute recurrent pancreatitis (ARP) recorded. Shotgun metagenomic sequencing was performed on extracted microbial DNA.

RESULTS: Microbial alpha diversity was lower for AP versus HC at all three time points (p < 0.008). Bray-Curtis ordinations showed the AP cohort did not cluster by time point, highlighting similarity in microbial composition over time. Within 12-month follow-up: 7/44 participants developed pre-DM/DM, 7/42 developed ARP, 16 had zero or one while 15 had multiple GI symptoms. Distinct clustering of samples was observed in the baseline samples of the group that developed ARP (p = 0.023) and in follow-up samples with multiple GI symptoms, p < 0.05. Relative abundance of most species was lower in AP samples when compared to HC at all time points with enrichment in Ruminococcus gnavus and Clostridium innocuum (AQ) (False Discovery Rate p < 0.05). Several pathways involved in protein biosynthesis were depleted in the AP cohort at all time points.

CONCLUSIONS: Gut dysbiosis persisted following AP in children at 3 and 12 months follow-up compared to HC. Microbiome signatures differed in the ARP cohort and those with multiple GI symptoms.}, } @article {pmid40901999, year = {2025}, author = {Prabakaran, R and Bromberg, Y}, title = {Deciphering enzymatic potential in metagenomic reads through DNA language models.}, journal = {Nucleic acids research}, volume = {53}, number = {16}, pages = {}, doi = {10.1093/nar/gkaf836}, pmid = {40901999}, issn = {1362-4962}, support = {80NSSC18M0093//NASA Astrobiology Institute/ ; 2310114//National Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Metagenome ; Molecular Sequence Annotation ; *Enzymes/genetics/metabolism ; Microbiota/genetics ; Software ; Sequence Analysis, DNA/methods ; }, abstract = {Microbial communities drive essential global processes, yet much of their functional potential remains unexplored. Metagenomics stands to elucidate this microbial "dark matter" by directly sequencing the microbial community DNA from environmental samples. However, the exploration of metagenomic sequences is mostly limited to establishing their similarity to curated reference sequences. A paradigm shift-language model (LM)-based methods-offers promising avenues for reference-free analysis of metagenomic reads. Here, we introduce two LMs, a pretrained foundation model REMME (Read EMbedder for Metagenomic Exploration), aimed at understanding the DNA context of metagenomic reads, and the fine-tuned REBEAN (Read Embedding-Based Enzyme ANnotator) for predicting the enzymatic potential encoded within the read-corresponding genes. By emphasizing function recognition over gene identification, REBEAN labels gene-encoded molecular functions of previously explored and new (orphan) sequences. Even though it was not trained to do so, REBEAN identifies the gene's function-relevant parts. It thus expands enzymatic annotation of unassembled metagenomic reads. Here, we present novel enzymes discovered using our models, highlighting model impact on our understanding of microbial communities.}, } @article {pmid40901884, year = {2025}, author = {Robes, JMD and Liebergesell, TCE and Beals, DG and Yu, X and Brazelton, WJ and Puri, AW}, title = {Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {36}, pages = {e2507323122}, doi = {10.1073/pnas.2507323122}, pmid = {40901884}, issn = {1091-6490}, support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; 2339190//National Science Foundation (NSF)/ ; LS-ECIAMEE-00006628//Simons Foundation (SF)/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; }, mesh = {*Methane/metabolism ; *Iron/metabolism ; *Metabolomics/methods ; Oxidation-Reduction ; Isotope Labeling/methods ; *Microbiota ; *Bacteria/metabolism/genetics ; Siderophores/metabolism ; Multigene Family ; }, abstract = {Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing-metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems.}, } @article {pmid40901853, year = {2025}, author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S}, title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331552}, doi = {10.1371/journal.pone.0331552}, pmid = {40901853}, issn = {1932-6203}, mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; }, abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.}, } @article {pmid40901000, year = {2025}, author = {Huang, F and Li, J and Liu, D and Li, Y and Tang, J}, title = {Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1642072}, doi = {10.3389/fcimb.2025.1642072}, pmid = {40901000}, issn = {2235-2988}, mesh = {Humans ; Infant, Newborn ; *Dysbiosis/microbiology/diagnosis/therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Infant, Newborn, Diseases/microbiology/diagnosis/therapy ; Precision Medicine/methods ; *Microbiota/genetics ; }, abstract = {The neonatal period is a critical stage for microbial colonization and immune system development, with dynamic changes in the microbiome closely linked to the pathogenesis of various diseases. Traditional microbiological testing methods have low sensitivity and time-consuming limitations compared to metagenomic next-generation sequencing (mNGS), which makes it difficult to meet the diagnostic and therapeutic needs of critically ill neonates. mNGS analyzes the total DNA in a sample without bias, allowing comprehensive identification of bacteria, viruses, fungi, and parasites, and resolution of functional genes, providing new avenues for precision diagnosis and treatment of diseases such as neonatal sepsis, necrotizing enterocolitis, neonatal pneumonia, neonatal meningitis, neonatal jaundice, and other diseases. However, challenges remain, including the need to optimize sample processing workflows and develop portable devices to enhance clinical conversion potential. In this review, we summarize the application, efficacy, and limitations of mNGS in neonatal diseases. This approach paves the way for novel avenues in mechanistic research, early diagnosis, and personalized therapy for these conditions.}, } @article {pmid40899487, year = {2025}, author = {Gu, T and Zerry, Y and Zhang, B and Tan, J and Taft, DH}, title = {Influence of Resistant Starch-Added Meat Analogs on the Resistome of Fecal Fermentations Using Human Gut Microbiota.}, journal = {Journal of food science}, volume = {90}, number = {9}, pages = {e70430}, doi = {10.1111/1750-3841.70430}, pmid = {40899487}, issn = {1750-3841}, support = {//University of Florida/ ; //U.S. Department of Agriculture/ ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Fermentation ; *Starch/metabolism ; Bacteria/genetics/classification/isolation & purification/drug effects/metabolism ; *Meat/analysis ; Adult ; Male ; Female ; *Resistant Starch ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Drug Resistance, Microbial ; Meat Substitutes ; }, abstract = {Meat analogs are emerging as a sustainable alternative to meat products, and novel meat analog products could potentially offer additional health benefits. Antimicrobial resistance (AMR) poses a serious threat to global human health. Dietary choices affect the composition of bacteria in the human gut microbiome and can influence the carriage of antimicrobial resistance genes (ARGs). Individuals with lower ARG carriage tend to consume more fiber, suggesting that novel fiber-rich meat analogs may help tackle the growing AMR crisis. We therefore hypothesized that adding resistant starch to meat analogs would reduce the number and abundance of ARGs in human gut microbial communities and tested this using in vitro fecal fermentation. Fecal samples were collected from three human donors. Meat analogs formulated from raw ingredients (pea, soy, and resistant starch)-including 100% pea, 90% pea and 10% resistant starch, 100% soy, and 90% soy and 10% resistant starch-served as the carbohydrate source for fecal fermentations. Whole metagenomic sequencing was performed on DNA from the fermentations. ANOVA showed significant differences in normalized ARG abundance by carbohydrate source (p = 0.021), though not in total ARG counts. Meat analogs with resistant starch resulted in a lower median normalized abundance of drug-resistant ARGs than meat analogs without resistant starch, but post-hoc testing could not determine which groups differed from each other due to limited sample size. Adding resistant starch to meat analogs is associated with reduced ARGs in human gut microbial communities, but more research is needed. PRACTICAL APPLICATIONS: Lowering the prevalence of antimicrobial resistance genes (ARGs) is an important public health goal, and emerging work suggests that diet may contribute to controlling the spread of ARGs. One association with diet and the resistome is a lower carriage of ARGs in individuals who consume more dietary fiber. This research therefore sought to pilot if adding resistant starch to meat analogs has the potential to reduce resistance gene carriage. The results found that adding resistant starch to plant-based meat products may help lower the abundance of antimicrobial resistance genes in the human gut microbiome. This provides the justification for larger scale studies and suggests that food manufacturers may be able to develop foods, including healthier meat alternatives, to assist in preserving the function of antibiotics for future generations.}, } @article {pmid40895054, year = {2025}, author = {Cárdenas-Hernández, V and Lemos-Lucumi, C and Toro-Perea, N}, title = {Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19728}, pmid = {40895054}, issn = {2167-8359}, mesh = {*Endophytes/genetics ; *Rhizophoraceae/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Plant Roots/microbiology ; Plant Leaves/microbiology ; Transcriptome ; Bacteria/genetics/classification ; Metagenome ; }, abstract = {The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.}, } @article {pmid40825855, year = {2025}, author = {Gopaulchan, D and Moore, C and Ali, N and Sukha, D and Florez González, SL and Herrera Rocha, FE and Yang, N and Lim, M and Dew, TP and González Barrios, AF and Umaharan, P and Salt, DE and Castrillo, G}, title = {A defined microbial community reproduces attributes of fine flavour chocolate fermentation.}, journal = {Nature microbiology}, volume = {10}, number = {9}, pages = {2130-2152}, pmid = {40825855}, issn = {2058-5276}, support = {133788//Innovate UK/ ; }, mesh = {*Chocolate/microbiology/analysis ; *Fermentation ; *Cacao/microbiology/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Microbiota ; Fungi/metabolism/genetics/classification/isolation & purification ; Colombia ; Hydrogen-Ion Concentration ; *Flavoring Agents/metabolism ; *Microbial Consortia ; Metagenomics ; Temperature ; Taste ; Food Microbiology ; }, abstract = {Cocoa (Theobroma cacao L.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics.}, } @article {pmid40787979, year = {2025}, author = {Liu, Y and Zhao, X and Feng, X and Zhu, W and Feng, S and Ren, M and Tu, Y and Niu, G and Zhu, Y}, title = {Diversity and evolutionary analysis of viruses carried by mosquitoes in Shandong, China.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0101825}, pmid = {40787979}, issn = {2165-0497}, support = {KY202422//the Suqian Science and Technology Program/ ; }, mesh = {Animals ; China ; Phylogeny ; *Culicidae/virology/classification ; *Mosquito Vectors/virology ; *Arboviruses/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Virome ; *Viruses/classification/genetics/isolation & purification ; Genetic Variation ; Biodiversity ; Evolution, Molecular ; Genome, Viral ; }, abstract = {UNLABELLED: Arboviruses represent a growing threat to global public health, as climate change is exacerbating the spread of these vectors and thereby increasing the transmission potential of arboviruses. As primary vectors, mosquitoes harbor remarkably diverse virus populations, broadly classified into mosquito-borne viruses and mosquito-specific viruses. Although metagenomic sequencing has revolutionized viral discovery, geographical variations in mosquito viromes remain poorly characterized. In this study, we conducted comprehensive viral surveillance on 5,051 mosquitoes representing six medically important species (grouped into 14 taxonomic units) collected from Shandong, China, in 2021. Using next-generation sequencing, we generated 3.7 billion clean reads and identified 10 distinct virus species spanning eight virus families. Phylogenetic analyses revealed substantial genomic diversity and complex evolutionary relationships, including two completely novel virus species and several incompletely characterized known viruses. Notably, Culex quinquefasciatus mosquitoes exhibited significantly greater viral diversity than other species, although we observed considerable overlap in viral communities across mosquito taxa, suggesting non-host-specific viral maintenance. The presence of two novel viruses in field populations was confirmed by RT-qPCR screening, wherein minimum infection rates of 0.16% and 0.38% were established. Our findings substantially expand the known diversity of mosquito-associated viruses in East Asia and provide critical baseline data for arbovirus surveillance programs. This work highlights the value of systematic virome characterization for predicting emerging arboviral threats and understanding virus-mosquito ecology in changing environments.

IMPORTANCE: Ten viruses, including two novel ones, were found in a study performed on mosquitoes in Shandong, China. It shows viral diversity and coexistence in different species, highlighting host impact on viral communities. The new viruses are prevalent locally, with infection rates of 0.38% and 0.16%. This work advances viral ecology understanding and has public health significance. This study sheds light on the circulation of the identified viruses in Shandong.}, } @article {pmid40778433, year = {2025}, author = {Li, W and Pan, S and Qian, J and Xia, Y and Han, G and Liu, J and Wang, Y and Peng, L and Huang, S and Chen, Y and Xie, Y and Xu, J and Zhang, W and Zhou, C}, title = {Comparisons of blood, upper respiratory tract and gut viromes from patients with lung cancer and healthy persons.}, journal = {International journal of cancer}, volume = {157}, number = {9}, pages = {1924-1938}, doi = {10.1002/ijc.70075}, pmid = {40778433}, issn = {1097-0215}, support = {TZKY20230204//Clinical Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; TZKY20230305//Key Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; 24142202800//Shanghai Science and Technology Innovation Action Plan/ ; 82341106//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Lung Neoplasms/virology/blood ; Male ; Female ; *Virome/genetics ; Middle Aged ; Aged ; Case-Control Studies ; Metagenomics/methods ; *Respiratory System/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; }, abstract = {Lung cancer is the leading cause of cancer-related mortality globally. Although some studies have proposed a potential association between viral infections and lung cancer pathogenesis, the evidence remains inconclusive. This study characterized the virome in blood, upper respiratory tract, and gut samples from 200 lung cancer patients and 75 healthy controls, with the goal of identifying potential microbial biomarkers for lung cancer, using viral metagenomics. Significant differences in viral diversity and composition were observed between cancer and healthy groups, with lower similarities in blood, respiratory, and gut viromes. Notably, LUSC and LUAD groups showed high similarity, with LUAD exhibiting the most diverse virome. In blood, Anelloviridae dominated in cancer patients, while Retroviridae was more abundant in specific subgroups. The upper respiratory tract virome in cancer patients was enriched with Siphoviridae and Myoviridae, contrasting with Retroviridae in healthy individuals. Gut viromes were dominated by Podoviridae and Virgaviridae in cancer patients, with Virgaviridae showing higher abundance compared to healthy controls. Alpha and beta diversity analyses indicated significant differences in blood and respiratory viromes but not in gut viromes. STAMP and LEfSe analyses identified Anelloviridae and Siphoviridae as potential biomarkers for lung cancer. Additionally, 242 anelloviruses with complete ORF1 were isolated, revealing high genetic diversity. These findings highlight distinct virome profiles in lung cancer patients, offering insights into potential diagnostic and therapeutic targets.}, } @article {pmid40759346, year = {2025}, author = {Zhao, C and Song, Y and Chen, H and Li, Y and Lei, A and Wu, Q and Zhu, L and He, Q}, title = {Study on the selective regulation of microbial community structure in microbial fuel cells by magnetic field-coupled magnetic carbon dots.}, journal = {Bioresource technology}, volume = {437}, number = {}, pages = {133065}, doi = {10.1016/j.biortech.2025.133065}, pmid = {40759346}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources/microbiology ; *Carbon/chemistry ; *Magnetic Fields ; RNA, Ribosomal, 16S/genetics ; Electricity ; Bacteria/genetics/metabolism ; *Quantum Dots/chemistry ; *Microbiota ; }, abstract = {Microbial fuel cells (MFCs), as a green energy technology that simultaneously enables electricity generation and wastewater treatment, exhibit performance that is highly dependent on the structural distribution of the microbial community. In this study, we investigated the effect of magnetic field (MF)-coupled magnetic carbon dots (N-CD/Fe3O4) as a selective pressure on the structure of mixed microbial communities in an intermittent pulsating fluidized-bed bioelectrochemical reactor. Under a moderate magnetic field (15 mT), N-CD/Fe3O4 were effectively adsorbed onto microbial cells and subsequently aggregated, significantly enhancing electron transfer within the community. The maximum power density reached 38.43 mW/m[2], which is about 5.07 times that of the blank control group. 16S rRNA and metagenomic analyses showed that the MF (15 mT) group exhibited significant enrichment of typical electroactive bacteria (40.32 %), such as Geobacter, which directly contributed to improved power production performance. In contrast, under a stronger magnetic field (60 mT), the abundance of typical electroactive bacteria (17.94 %) decreased, while atypical electroactive (38 %) and metabolically complementary bacteria that facilitate syntrophic cooperation (42.85 %) showed adjusted abundances, forming a functionally more balanced microbial community with improved adaptability to real wastewater conditions. This study demonstrates that by tuning magnetic field intensity and coupling with magnetic carbon dots, the structure and function of microbial communities can be directionally regulated, providing an effective strategy for developing electroactive inocula with enhanced power generation and wastewater adaptability.}, } @article {pmid40748195, year = {2025}, author = {Bai, S and Wang, Z and Guo, Y and Xu, H and Li, J and Peng, X}, title = {Iron is an important influence of volcanic ash input on the evolution of deep-sea ecosystems.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0071525}, pmid = {40748195}, issn = {2165-0497}, mesh = {*Volcanic Eruptions/analysis ; *Iron/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; *Seawater/microbiology/chemistry ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Ecosystem ; Microbiota ; Metagenomics ; Metagenome ; }, abstract = {UNLABELLED: Volcanoes, originating from deep-seated magmatic activity, serve as crucial conduits connecting Earth's interior and surface. Volcanic eruptions, a primary manifestation of this connection, exert profound influence across Earth's surface systems. Volcanic ash, a significant product of these eruptions, has long been a focal point of Earth science research due to its far-reaching impacts. However, the challenges associated with deep-sea sampling and a relative lack of interdisciplinary collaboration have hindered our understanding of how volcanic ash deposition affects the abyssal environment. Here, leveraging a combined geological and microbiological approach, we investigated sediments within the Kermadec Trench impacted by rhyolitic volcanic ash. Our findings demonstrate that iron availability is the primary driver of microbial community structure in these ash-influenced deep-sea sediments. The mantel test analysis further revealed that four key categories of iron-related functional genes involved in iron acquisition (heme transport, iron transport, and siderophore transport) and iron storage significantly shape the resident microbial communities. Furthermore, metagenomic binning yielded numerous refined metagenome-assembled genomes (MAGs) from these deep-sea sediments, all of which harbored iron-related functional genes. Viral metagenomic analysis suggests that viruses in these sediments do not directly influence abyssal prokaryote-mediated iron cycling through the carriage of iron-related auxiliary genes. Instead, viral lysis of iron-cycling prokaryotes appears to be a key regulatory mechanism. These results provide critical new data and insights into microbial iron cycling in the deep sea under the influence of volcanic ash deposition.

IMPORTANCE: Volcanic eruptions emit vast amounts of ash, which eventually settle in the deep ocean. This study explores how the deposition of volcanic ash influences deep-sea microbial communities, primarily through iron enrichment. Our findings highlight the pivotal role of iron-related genes in shaping these communities, while viruses may play an indirect role in modulating iron cycling. These insights enhance our understanding of how volcanic activity affects deep-sea ecosystems and biogeochemical cycles. By elucidating the intricate link between volcanic ash, iron availability, and microbial dynamics, this research provides a novel perspective on how geological processes drive life in the deep ocean. Ultimately, this knowledge contributes to a deeper understanding of global nutrient cycles.}, } @article {pmid40744840, year = {2025}, author = {Zhan, J and Cheng, B and Guo, K and Tao, X and Cai, X and Li, Z and Tang, Z and Zhan, J and Wu, C}, title = {Absolute quantitative metagenomic analysis reveals unique gut bacteria underlying berberine and metformin's anti-metabolic disorders effects.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0008425}, pmid = {40744840}, issn = {2165-0497}, mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Metformin/pharmacology ; Animals ; Mice ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metabolic Diseases/drug therapy/microbiology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Feces/microbiology ; }, abstract = {This study aimed to evaluate the potential functional bacteria in the efficacy of two drugs in ameliorating diet-induced metabolic disorder model using absolute and relative quantification methods and to evaluate the benefit of absolute quantification compared with relative quantification. The gut microbiota is implicated in the pathogenesis of various chronic diseases, including diet-induced metabolic disorder model. Berberine (BBR) and metformin (MET) are commonly used in the clinical management of metabolic disorder, yet their effects on gut microbiota regulation differ. This study employs both relative and absolute quantitative methods to assess the differential impacts of these drugs on the modulation of gut microbiota in metabolic disorder mice. Both BBR and MET effectively ameliorate the condition of metabolic disorder. While some relative quantitative sequencing results contradicted the absolute sequencing data, the latter was more consistent with the actual microbial community composition. Absolute quantitative sequencing provides a more accurate reflection of the drug's effects. Notably, both absolute and relative quantitative sequencing demonstrated an upregulation of Akkermansia.IMPORTANCEOur study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.}, } @article {pmid40704918, year = {2025}, author = {Pan, J and Tian, X and Wu, K and Ji, J and Dong, M and Sun, T and Lv, D and Yao, P and Lv, L and Yao, H}, title = {Gut microbiota-associated non-cholesterol sterol dysregulation modulates immune reconstitution during antiretroviral therapy in people living with HIV.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0140425}, pmid = {40704918}, issn = {2165-0497}, support = {2024YFC2309900//National Key Research and Development Program of China/ ; 2022R52029//Zhejiang Plan for the Special Support fort Top-notch Talents/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; SYS202202//Shandong Provincial Laboratory Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/immunology/microbiology ; Male ; Leukocytes, Mononuclear/immunology ; Adult ; Female ; *Sterols/metabolism ; Middle Aged ; CD4-Positive T-Lymphocytes/immunology ; Dysbiosis/microbiology/immunology ; Phytosterols/metabolism ; }, abstract = {Non-cholesterol sterol metabolism plays a crucial role in immune regulation. However, the non-cholesterol sterol profiles, its association with gut dysbiosis, and its impact on the CD4[+] T cell recovery in people living with HIV (PLWH) are yet to be elucidated. In this study, we recruited 37 PLWH and 50 healthy controls to characterize non-cholesterol sterol profiles and gut microbiota composition using targeted liquid chromatography-mass spectrometry and metagenomic analysis. Correlations between sterol profiles and immune cell subsets were assessed. In vitro peripheral blood mononuclear cell (PBMC) model was used to validate key findings. We identified a distinct dysregulation of non-cholesterol sterol metabolism in PLWH, characterized by elevated levels of cholesterol precursors and metabolites and depleted levels of plant sterols, which were linked to gut dysbiosis. Our study results highlighted Oscillibacter spp. as the key regulator of sterol metabolism. Specifically, plant sterols (e.g., brassicasterol and campesterol) were found to be associated with impaired CD4[+] T cell recovery during antiretroviral therapy (ART). These findings were validated using ex vivo PBMC models, which revealed that brassicasterol stimulates T cell abnormal activation and pro-inflammatory cytokine release, whereas lathosterol dampens immune activation and inflammation. In summary, our study highlights the interplay between gut dysbiosis and sterol dysregulation in PLWH, demonstrating that higher brassicasterol levels impair immune recovery post-ART by promoting CD4[+] T cell hyperactivation. Hence, targeting microbial sterol metabolism-through Oscillibacter spp. enrichment or plant sterol modulation-may offer novel therapeutic strategies to optimize ART outcomes by balancing immune activation and resolution.IMPORTANCEThis study is the first to integrate non-cholesterol sterol profiling with gut microbiota analysis in people living with HIV (PLWH), uncovering a unique sterol dysregulation characterized by elevated cholesterol precursors and depleted plant sterols in this population. We demonstrate that Oscillibacter spp. were associated with these metabolic shifts and that specific sterols differentially affect immune recovery: plant sterols such as brassicasterol impede CD4[+] T cell restoration by promoting hyperactivation, whereas the cholesterol derivative lathosterol mitigates inflammation and supports immune reconstitution. These insights reveal novel microbiome-sterol interactions that can be leveraged to develop targeted microbiome- and sterol-based interventions aimed at enhancing antiretroviral therapy efficacy and long-term immune health in PLWH.}, } @article {pmid40698938, year = {2025}, author = {Lei, L and Li, X and Xiong, Z and Li, J and Liu, L and Chen, L and Zhong, Q and Jiang, H and Cheng, Z and Xiao, S}, title = {Distinctive structure of endophytic microbial communities in two species of wild and cultivated rice.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0297824}, pmid = {40698938}, issn = {2165-0497}, support = {202205AR070001-01//Yunnan seed Laboratory/ ; 202205AM340037//Science and technology personnel/ ; 2021YFD1200100//National Key Research and Development Program of China/ ; SKL-KF-202325//Open Research Fund of State Key Laboratory of Bioelectronics/ ; }, mesh = {*Oryza/microbiology/classification/growth & development ; *Endophytes/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; China ; Plant Leaves/microbiology ; Metagenomics ; Phylogeny ; }, abstract = {Endophytic microbial communities play an important role in plant development, nutrient acquisition, and oxidative stress tolerance. Oryza officinalis and Oryza meyeriana are unique wild rice varieties in China with many high-quality resistance genes, rich endophyte diversity, and potential resources for sustainable agriculture. In the present study, the endophytic microbial community structures of O. officinalis, O. meyeriana, and cultivated rice were compared using metagenomic sequencing. Dechloromonas, Salmonella, Klebsiella, and Listeria were the core microbial groups in wild and cultivated rice. The relative abundances of Ligilactobacillus, Escherichia, and Bradyrhizobium in O. meyeriana were higher than those in cultivated rice. The relative abundances of Listeria, Acinetobacter, Escherichia, and Dechloromonas in O. officinalis were also higher. Compared to that of cultivated rice, the microbiota of wild rice had a more complex and stable community network. At the pathway level 2 based on the Kyoto Encyclopedia of Genes and Genomes classification system, the relative abundance of metabolic categories was dominant. Most pathways showed that the O. officinalis relative abundance was higher than those of the other two species. Our study revealed differences in the leaf endophyte community structure and function between wild and cultivated rice in the same habitat, demonstrating the potential of wild rice in recruiting specific microorganisms to improve crop performance and promote safe and sustainable food production.IMPORTANCEUnder the current climate change environment, plant-beneficial endophytes are of great significance for promoting food production. Modern cultivars may have lost many beneficial endophytes compared to their ancestors. However, relatively few studies have been conducted on the community structure and function of modern ancestral crop endophytes. In this study, the composition and function of the microbial communities of two wild rice species were analyzed; the differences between them and cultivated rice were determined; and the patterns of microbial interactions and their core microbiomes were determined. Our findings can aid in the exploration of the beneficial endophytes in wild rice and use them to improve crop stress resistance and sustainability. These results provide relevant insights into the role of endophytes in the mechanism of high-stress resistance in wild rice.}, } @article {pmid40614652, year = {2025}, author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T}, title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.}, journal = {Poultry science}, volume = {104}, number = {9}, pages = {105488}, pmid = {40614652}, issn = {1525-3171}, mesh = {Animals ; Kazakhstan ; *Chickens/microbiology ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/isolation & purification/classification/genetics ; *Microbiota ; *Metagenome ; }, abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.}, } @article {pmid40580838, year = {2025}, author = {Mirzaei, S and Gorczyca, B and Uyaguari-Diaz, M and Sparling, R and Maksimova, E}, title = {Microbial consortia in full-scale pre-ozonated biologically active filters treating a high-DOC water: Effects of seasonal and operational variations.}, journal = {Water research}, volume = {285}, number = {}, pages = {124065}, doi = {10.1016/j.watres.2025.124065}, pmid = {40580838}, issn = {1879-2448}, mesh = {*Seasons ; *Water Purification/methods/instrumentation ; *Filtration/methods/instrumentation ; *Microbial Consortia ; Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; *Carbon ; Charcoal/chemistry ; }, abstract = {This study investigated the microbial dynamics in full-scale biologically active anthracite/silica sand (BAS) and granular activated carbon (BAC) filters used to treat high-DOC coagulated softened water. By analyzing these filter types across two seasons (winter and summer), we examined the impact of operational conditions-including temperature (1 °C vs. 25 °C), backwashing cycle (72 h vs. two weeks), and empty bed contact time (10 vs. 24 min in BAC and 4 vs. 10 min in BAS)-on organic matter removal, biological activity, and bacterial taxonomy and functionality. The highest DOC (19.1 %) and BDOC (34.8 %) removal rates were observed in BAC during summer and post-backwashing, whereas BAS in both seasons and BAC in the winter showed minimal effects on the organic matter concentration. No direct correlation was found between ATP levels, bacterial 16S rRNA bacterial gene copy numbers, and DOC/BDOC removal in BAC. However, an optimal condition of 13 × 10[-6] ATP per bacterial gene copy number in BAC during summer post-backwashing coincided with the highest DOC and BDOC removal. Bacterial taxa with established associations to DOC degradation accounted for over 60 % of the total bacterial orders identified in both BAS and BAC across seasons. The BAC environment appeared to selectively enrich consortia capable of transforming complex DOC fractions, likely facilitated by its greater surface area, extended EBCT, and less frequent backwashing. These conditions supported the persistence and activity of specific bacterial orders, including Actinomycetales, Myxococcales, Planctomycetales, and Rhizobiales. Subsystem-level metagenomic analysis indicated a significant enrichment of genes associated with metabolic functions linked to enzymes such as decarboxylase, N-methylhydantoinase A, cyclic beta-1,2-glucan synthase, carbon monoxide dehydrogenase, cell division protein FtsH, N-methylhydantoinase B, and UDP-glucose 4-epimerase in BAC samples. This study deepens our understanding of the BAF microbiome's role in natural organic matter removal and its relationship with operational parameters, addressing critical gaps in drinking water biological treatment.}, } @article {pmid40578104, year = {2025}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.}, journal = {Water research}, volume = {285}, number = {}, pages = {124074}, doi = {10.1016/j.watres.2025.124074}, pmid = {40578104}, issn = {1879-2448}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Temperature ; *Catfishes/microbiology ; Aquaculture ; Bacteria/genetics ; }, abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.}, } @article {pmid40570497, year = {2025}, author = {Thornton, M and Eder, G and Amman, F and Pantielieieva, A and Vierheilig, J and Bergthaler, A}, title = {Comparative wastewater virome analysis with different enrichment methods.}, journal = {Water research}, volume = {285}, number = {}, pages = {123985}, doi = {10.1016/j.watres.2025.123985}, pmid = {40570497}, issn = {1879-2448}, mesh = {*Wastewater/virology ; *Virome ; Ultrafiltration ; Viruses/isolation & purification ; }, abstract = {Wastewater-based epidemiology (WBE) has proven its value for public health. Physical concentration of virus particles is a crucial step for WBE to permit a sensitive and unbiased characterization of the catchment virome. Here we evaluate five different virion concentration techniques, including polyethylene glycol precipitation (PEG), vacuum-based direct capture (VDC), ultrafiltration (UF), NanoTrap® (NT), and membrane adsorption (MEM) for their suitability to concentrate a wide variety of viral taxa from raw wastewater for PCR detection and sequencing-based metagenomic readouts. We found that to capture a taxonomically diverse virome from wastewater, PEG and VDC outperform all other methods tested in enrichment rates, reproducibility, species detection, and captured nucleotide diversity. We observed that different methods exhibit variable concentration efficiencies across taxonomic groups in a reproducible manner, though we could not identify common physiochemical attributes driving this difference. We conclude that both PEG and VDC are equally capable at detecting and enriching a broad range of viral taxa, boosting the genomic information potential and reducing blind spots relative to other tested methods. These results advance WBE towards capturing the complex wastewater virome and help guide protocol choices for potential future viral threats.}, } @article {pmid40561629, year = {2025}, author = {Deng, Z and Xie, Y and Yu, H and Zhang, X and Tan, T and Kuang, W and Han, Z and Li, Y and Wang, H and Zhang, N and Zhang, C}, title = {Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights.}, journal = {Water research}, volume = {285}, number = {}, pages = {124072}, doi = {10.1016/j.watres.2025.124072}, pmid = {40561629}, issn = {1879-2448}, mesh = {*Microbiota ; Halogenation ; *Seawater/microbiology ; Genomics ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; }, abstract = {Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 h. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced beta diversity (community composition) but had only a minor effect on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05 % yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1 % to 32 %). Comparative genomic analysis indicated that Bin3 has undergone specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.}, } @article {pmid40544677, year = {2025}, author = {Bortoluzzi, C and Watson, M and Iuspa, MA and Lumpkins, B and Mathis, G and Jones, M and Hofacre, C}, title = {Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges.}, journal = {Poultry science}, volume = {104}, number = {9}, pages = {105454}, pmid = {40544677}, issn = {1525-3171}, mesh = {Animals ; *Chickens/growth & development/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Poultry Diseases/microbiology/prevention & control/parasitology ; Animal Feed/analysis ; Diet/veterinary ; Clostridium perfringens/physiology ; Dietary Supplements/analysis ; Coccidiosis/veterinary/prevention & control ; Clostridium Infections/veterinary/microbiology/prevention & control ; Eimeria/physiology ; *Enteritis/veterinary/microbiology/prevention & control ; *Polysaccharides/administration & dosage/metabolism ; Fatty Acids, Volatile/metabolism ; Random Allocation ; Male ; Necrosis/veterinary/microbiology ; Cecum/microbiology ; }, abstract = {Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy development and functionality of the gastrointestinal tract (GIT) in chickens. Our hypothesis was that adding a glycan-based PB to the diet would steer microbial metabolism towards increased SCFA production in the ceca, thereby reducing the adverse effects of necrotic enteritis (NE) in chickens. These studies evaluated the supplementation of PB on the cecal microbiome and growth performance in broiler chickens exposed to a necrotic enteritis (NE) challenge. Experiment 1: Day-old chicks were assigned to three treatment groups: a control, a challenged control, and a challenged group supplemented with PB. The birds were vaccinated for coccidiosis at day 0 and challenged with Clostridium perfringens. Cecal content was collected from one bird per pen on days 22 and 42 for microbiome analysis. Experiment 2: Day-old chicks were again assigned to three treatments: control, challenged control, and challenged with PB. All birds were vaccinated for coccidiosis and challenged with Eimeria maxima on day 14 and later with C. perfringens. On day 21, birds were euthanized for NE lesion scoring. In Exp. 1, the supplementation of PB significantly improved (P < 0.05) the growth performance of the challenged birds. An increased relative abundance of species related to SCFA production was observed on day 42, including several Faecalibacterium species (P < 0.05). This was paired with an increased relative abundance of both propionate (P<0.05) and butyrate pathways in birds with PB supplementation. In Exp. 2, on day 21, the challenge impaired growth performance, but the supplementation of PB counteracted this effect (P < 0.05). On day 42, the supplementation of PB improved BW by 10 % (P < 0.0001), and the FCR by 8.4 % (P < 0.0001) when compared to the challenged group. The supplementation of PB reduced NE associated mortality (5.5 vs 0.5 %; P = 0.002) and reduced the lesions characteristic of NE (P < 0.0001). Taken together, the microbiome metabolic shift observed with the supplementation of PB explains the improvement in growth performance, resilience to enteric stress and faster recovery of the intestine, which consequently improves welfare and the sustainability of poultry production.}, } @article {pmid40482531, year = {2025}, author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X}, title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.}, journal = {Poultry science}, volume = {104}, number = {9}, pages = {105360}, pmid = {40482531}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Diet/veterinary ; *Diet, Vegetarian/veterinary ; Liver/pathology/drug effects ; Random Allocation ; Male ; Animal Nutritional Physiological Phenomena ; }, abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.}, } @article {pmid40482059, year = {2025}, author = {Rendina, M and Turnbaugh, PJ and Bradley, PH}, title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {9}, pages = {}, doi = {10.1093/g3journal/jkaf131}, pmid = {40482059}, issn = {2160-1836}, support = {R35GM151155/NH/NIH HHS/United States ; R01CA255116/NH/NIH HHS/United States ; R01HL122593/NH/NIH HHS/United States ; }, mesh = {Humans ; *Xenobiotics/metabolism ; *Gastrointestinal Microbiome/genetics ; Animals ; }, abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; 2 of these, 6-mercaptopurine by xanthine dehydrogenase and 5-fluorouracil by dihydropyrimidine dehydrogenase, have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.}, } @article {pmid40892742, year = {2025}, author = {Zhu, J and Chen, Y and Han, Y and Li, J}, title = {Mechanism of Huanglian Wendan Decoction in ameliorating non-alcoholic fatty liver disease via modulating gut microbiota-mediated metabolic reprogramming and activating the LKB1/AMPK pathway.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0331303}, pmid = {40892742}, issn = {1932-6203}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Rats ; Male ; *AMP-Activated Protein Kinases/metabolism ; Rats, Sprague-Dawley ; Signal Transduction/drug effects ; *Protein Serine-Threonine Kinases/metabolism ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects/pathology ; AMP-Activated Protein Kinase Kinases ; Disease Models, Animal ; Carnitine O-Palmitoyltransferase/metabolism ; Metabolic Reprogramming ; }, abstract = {BACKGROUND: Huanglian Wendan Decoction (HLWDD), a classical traditional Chinese medicine (TCM) formula, has shown therapeutic promise in treating metabolic disorders. However, its underlying mechanisms against non-alcoholic fatty liver disease (NAFLD) remain unclear.

OBJECTIVE: This study aimed to elucidate the pharmacological mechanisms by which HLWDD ameliorates NAFLD, focusing on its impact on lipid metabolism, gut microbiota, and amino acid regulation.

METHODS: A NAFLD rat model was established by administering a high-sugar, high-fat, high-salt diet for 20 weeks. The core components of HLWDD were identified and quantified using UPLC-Q-TOF-MS/MS and HPLC, and further validated via network pharmacology and molecular docking. Therapeutic efficacy was assessed through analysis of body weight, serum lipid profiles, inflammatory cytokines, hepatic histology, and protein expression. Gut microbiota composition and liver-intestine metabolite profiles were evaluated using metagenomic sequencing and LC-MS/MS.

RESULTS: Seven key constituents, including quercetin and berberine, were quantified (15.11-164.37 μg/mL) and shown to interact with lipid metabolism targets such as liver kinase B1 (LKB1), AMP-activated protein kinase (AMPK), peroxisome proliferator-activated receptor alpha (PPARα), and carnitine palmitoyltransferase 1A (CPT1A). HLWDD treatment significantly reduced body weight, hepatic lipid accumulation, and serum levels of triglycerides, total cholesterol, and low-density lipoprotein cholesterol, while increasing high-density lipoprotein cholesterol. Proinflammatory cytokines (IL-6, IL-1β, TNF-α) were notably suppressed. Mechanistically, HLWDD activated the LKB1/AMPK signaling pathway and modulated aspartic acid metabolism in association with increased abundance of Akkermansia in the gut. Metabolomic analysis identified 13 differential metabolites, with aspartic acid showing strong correlations with Akkermansia and LKB1/AMPK activity.

CONCLUSION: HLWDD exerts its anti-NAFLD effects by enhancing Akkermansia-mediated aspartate metabolism, thereby activating the LKB1/AMPK axis and promoting lipid oxidation via CPT1A and PPARα. This study provides new mechanistic insight into the gut-liver axis in NAFLD and highlights HLWDD as a multi-targeted therapeutic approach for restoring metabolic balance.}, } @article {pmid40890888, year = {2025}, author = {Wang, S and Zhao, Z and Cheng, R and Cui, L and Wang, J and Rubin-Blum, M and Zhang, Y and Liu, B and Chen, X and Baltar, F and Cao, X and Wen, X and Alain, K and Chen, Z and Liao, J and Jiang, L and Shao, Z}, title = {Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {194}, pmid = {40890888}, issn = {2049-2618}, support = {42306127//National Natural Science Foundation of China/ ; 42306127//National Natural Science Foundation of China/ ; 42176134//National Natural Science Foundation of China/ ; 42030412//National Natural Science Foundation of China/ ; 2024002//Scientific Research Foundation of Third Institute of Oceanography/ ; 2019021//Scientific Research Foundation of Third Institute of Oceanography/ ; }, mesh = {*Geologic Sediments/microbiology ; *Carbon Cycle ; Wetlands ; Phylogeny ; China ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Carbon/metabolism ; Metagenomics/methods ; Gammaproteobacteria/metabolism/genetics/classification/isolation & purification ; Microbiota ; }, abstract = {BACKGROUND: Mangroves are hotspots of carbon sequestration in transitional zones between marine and terrestrial ecosystems. Microbially driven dark carbon fixation (DCF) is prominent in sediments, yet our understanding of the DCF process across this continuum remains limited. In this study, we explored DCF activities and associated chemoautotrophs along the sediment depth of different mangrove sites in Fujian Province, China, using radiocarbon labeling and molecular techniques.

RESULTS: Our results showed that the DCF rates ranged from 0.02 to 3.27 mmol C m[-2] day[-1] in all samples, showing a depth-dependent spatial variation. These rates of DCF were closely related to the environmental factors such as DIC, TS, AVS, NH4[+], NO3[-], and NO2[-]. Metagenomic analysis revealed six carbon-fixing pathways, with the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway being predominant. Further analysis of MAGs revealed that Gammaproteobacteria, Desulfobacteria, and Campylobacteria were the most abundant carbon-fixing groups. Intriguingly, some new lineages were found to have carbon-fixing potential, including two candidatus taxa JAJVIF01 and BMS3Abin14. Metatranscriptomic analyses confirmed that these carbon-fixing microbes were active in situ and occupied different niches. In the surface layers, Gammaproteobacteria with the CBB cycle played an important role in DCF, mainly driven by sulfur and hydrogen oxidation with oxygen reduction; in the deeper layers, Campylobacteria with the reductive tricarboxylic acid (rTCA) cycle and Desulfobacteria with the WL pathway were active members for DCF, mainly through sulfur, hydrogen, and CO oxidation. While in the deepest layers of 18-20 cm, methane-producing archaea Methanosarcinia was the essential member driving DCF. In addition, most taxa containing the WL pathway displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies.

CONCLUSIONS: Overall, this study provides new insights into the understanding of biological carbon fixation and its ecological functions in mangrove sediments. Video Abstract.}, } @article {pmid40890809, year = {2025}, author = {Xue, S and Shi, T and Xie, J and Liu, W and Yao, S and Li, N and Liu, H and Kong, W and Gao, F}, title = {Integrated fecal macrogenomic and metabolomic analyses reveal celiac disease flora and metabolic profiles associated with Chinese populations.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {972}, pmid = {40890809}, issn = {1479-5876}, support = {2022D01C831//Natural Science Foundation of Xinjiang/ ; 82260116//National Natural Science Foundation of China/ ; 82460117//National Natural Science Foundation of China/ ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Case-Control Studies ; *Celiac Disease/ethnology/genetics/metabolism/microbiology ; China/ethnology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Metabolome ; *Metabolomics ; East Asian People ; }, abstract = {BACKGROUND AND AIMS: Genes and gluten intake are necessary but not sufficient to cause celiac disease (CeD), and altered intestinal flora is an additional risk factor for the development of CeD. The present study was conducted to investigate the intestinal flora and metabolic characteristics of CeD among the Chinese population, with the use of CeD patients from Xinjiang, China.

METHODS: Macrogenomic sequencing was performed to analyze the composition and differences of the intestinal flora of 40 CeD patients and 40 healthy subjects. Non-targeted metabolomics analysis was carried out using LC-MS metabolomics technology in 30 CeD patients and 30 control subjects. A model for CeD diagnosis was constructed based on differential flora and metabolites. Blood was collected from all subjects for HLA typing assay.

RESULTS: CeD-associated alterations were identified in the gut microbiome and metabolome. 15 differential bacterial strains (AUC = 0.85) and 8 differential metabolites (AUC = 0.9799) constructed a diagnostic panel that was effective in differentiating CeD patients from healthy subjects. Compared with non-CeD patients carrying HLA-DQ[±], the abundances of Agathobacter_rectalis, Bifidobacterium_pseudocatenulatum, Clostridia_bacterium, Coprococcus_comes, and Fusicatenibacter_saccharivorans in CeD patients were significantly lower (P < 0.05). Metabolomics analysis showed that Leoheteronin D, Pc (34:2), and GPEtn (18:1/16:0) were the major metabolites involved in multiple metabolic pathways in CeD patients.

CONCLUSION: Our study revealed specific alterations in the gut microbiome and metabolome of Chinese CeD patients through a multi-omics integration strategy. We found that CeD individuals carrying CeD risk genes may possess a unique intestinal flora composition, and this intestinal flora may, to some extent, explain the pathogenesis of CeD beyond the contributions of genes and gluten intake.}, } @article {pmid40719501, year = {2025}, author = {Keskey, R and Bluiminck, S and Sangwan, N and Meltzer, R and Lam, A and Thewissen, R and Zaborin, A and van Goor, H and Zaborina, O and Alverdy, J}, title = {Dietary impact on the gut resistome: western diet independently increases the prevalence of antibiotic resistance genes within the gut microbiota.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0276624}, pmid = {40719501}, issn = {2165-0497}, support = {R01GMO62344-22//HHS | NIH | OSC | Common Fund (NIH Common Fund)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Diet, Western/adverse effects ; Cecum/microbiology ; *Bacteria/genetics/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Mice, Inbred C57BL ; Male ; }, abstract = {Approximately half of surgical site infections are caused by pathogens resistant to the antibiotics used for prophylaxis. We recently demonstrated that when mice are fed a western diet (WD) that is high in fat and low in fiber, exposed to antibiotics, and undergo an otherwise recoverable surgery, they develop lethal sepsis associated with dissemination of multi-drug-resistant pathogens. Here, we hypothesized that a WD alone can drive the intestinal microbiome to become populated by antibiotic-resistant bacteria independent of exposure to antibiotics. The cecal microbiota response to antibiotics was determined utilizing Biolog Phenotype Microarrays in the presence of 48 different antibiotics. WD-fed mice had a significant increase in antibiotic resistance within their microbiome compared to mice on a standard low-fat, high-fiber diet (SD) including aminoglycosides, tetracyclines, cephalosporins, fluoroquinolones, and sulfamethoxazole. By metagenomic sequencing, there was an increase in the antibiotic resistance genes (ARGs) within the WD cecal microbiota, including CfxA2, ErmG, TetQ, and LnuC. After just 7 days of WD, the ARGs ErmG and CfxA2 were detectable within the stool. WD independent of antibiotic exposure increases the presence of ARGs within the gut microbiota independent of antibiotic exposure.IMPORTANCEAntibiotic resistance is a major challenge in healthcare and results in significant morbidity and mortality. Currently, half of surgical site infections are caused by pathogens resistant to antibiotics used for prophylaxis. In this study, we demonstrate that a western diet alone has the ability to increase the presence of antibiotic resistance genes within the gut microbiome. By understanding dietary influences on the gut resistome, we may improve our understanding of infections with antibiotic-resistant organisms and one day develop personalized antibiotic regimens based on an individual's gut resistome.}, } @article {pmid40711419, year = {2025}, author = {Licata, AG and Zoppi, M and Dossena, C and Rossignoli, F and Rizzo, D and Marra, M and Gargari, G and Mantegazza, G and Guglielmetti, S and Bergamaschi, L and Nigro, O and Chiaravalli, S and Massimino, M and De Cecco, L}, title = {QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.}, journal = {Microbiology spectrum}, volume = {13}, number = {9}, pages = {e0167325}, pmid = {40711419}, issn = {2165-0497}, support = {//Bain Capital Children's Fund Europe/ ; ID NET-2019-12371188//Italian Ministry of Health/Regione Lombardia/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; Feces/microbiology ; Software ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Child ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; *Computational Biology/methods ; }, abstract = {Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-caregiver microbial relationships. We generated 16S rRNA profiles from 5 mock communities and 12 child-caregiver fecal sample pairs. Benchmarking against commercial software showed that the multi-region (V2-9) approach produced microbial profiles nearly identical to proprietary outputs, with higher sequencing depth and improved taxonomic resolution compared to single-region analyses. Both approaches demonstrated similar microbial richness, accurate mock community reconstruction, and high reproducibility (R = 0.99, P < 0.0001). These findings were further validated using fecal samples. Application of the pipeline to pediatric samples revealed distinct, differentially abundant Bifidobacterium bifidum and Bifidobacterium adolescentis variants in children whose microbiota closely resembled that of their caregivers. Overall, this study presents a validated, open-source QIIME2 and R pipeline for multi-amplicon sequencing, providing a standardized and reproducible framework for 16S rRNA gene profiling in clinical and research contexts.IMPORTANCEMulti-amplicon sequencing comprehensively characterizes microbial communities by targeting multiple regions of the 16S rRNA gene. However, analytical workflows and reference databases provided by commercial library preparation kits frequently rely on proprietary primers and closed-source pipelines, which can limit transparency, reproducibility, and adaptability. To address these limitations, we developed and validated an open-source bioinformatics pipeline utilizing QIIME2 and R. Our pipeline integrates data from all targeted 16S regions, generating microbial profiles comparable to those produced by proprietary software. Validation was performed using mock samples and fecal samples collected from pediatric cancer patients and their caregivers, confirming the pipeline's reliability and broad applicability. Furthermore, our pipeline enables detailed analysis of microbial variants, surpassing traditional genus-level restrictions and fully leveraging the enhanced coverage offered by multi-amplicon sequencing. Our findings highlight the necessity of adopting open-source solutions to ensure scientific reproducibility and adaptability to emerging methodologies.}, } @article {pmid40377870, year = {2025}, author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM}, title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {4}, pages = {1938-1968}, pmid = {40377870}, issn = {1867-1314}, mesh = {Humans ; *Gene Editing/methods ; *Neoplasms/microbiology/therapy/drug therapy ; *Microbiota ; *Antimicrobial Peptides/pharmacology ; CRISPR-Cas Systems ; Animals ; *Drug Resistance, Microbial ; Clustered Regularly Interspaced Short Palindromic Repeats ; }, abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.}, } @article {pmid39641861, year = {2025}, author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H}, title = {Probiotic Mixture Attenuates Colorectal Tumorigenesis in Murine AOM/DSS Model by Suppressing STAT3, Inducing Apoptotic p53 and Modulating Gut Microbiota.}, journal = {Probiotics and antimicrobial proteins}, volume = {17}, number = {4}, pages = {2227-2243}, pmid = {39641861}, issn = {1867-1314}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; *Colorectal Neoplasms/drug therapy/chemically induced/microbiology/metabolism ; Mice ; *Tumor Suppressor Protein p53/metabolism/genetics ; *STAT3 Transcription Factor/metabolism/genetics ; Apoptosis/drug effects ; Dextran Sulfate/adverse effects ; Azoxymethane/adverse effects ; Carcinogenesis/drug effects ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide. The standard CRC chemo drug, 5-Fluorouracil (5-FU), has a poor response rate and chemoresistance, prompting the need for a more effective and affordable treatment. In this study, we aimed to evaluate whether Prohep, a novel probiotic mixture, would alleviate azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colorectal tumorigenesis and enhance 5-FU efficacy and its mechanism. Our results suggested that Prohep showed stronger anti-tumorigenesis effects than 5-FU alone or when combined in the AOM/DSS model. Prohep significantly reduced the total tumor count, total tumor size, caecum weight, colonic crypt depth, colonic inflammation, and collagen fibrosis. Prohep downregulated pro-inflammatory TNF-α and proliferative p-STAT3 and upregulated apoptotic p53. Metagenomics analysis indicated that Prohep-enriched Helicobacter ganmani, Desulfovibrio porci, Helicobacter hepaticus, and Candidatus Borkfalkia ceftriaxoniphila were inversely correlated to the total tumor count. In addition, Prohep-enriched Prevotella sp. PTAC and Desulfovibrio porci were negatively correlated to AOM/DSS enriched bacteria, while forming a co-existing community with other beneficial bacteria. From KEGG analysis, Prohep downregulated CRC-related pathways and enhanced pathways related to metabolites suppressing CRC like menaquinone, tetrapyrrole, aminolevulinic acid, and tetrahydrofolate. From Metacyc analysis, Prohep downregulated CRC-related peptidoglycan, LPS, and uric acid biosynthesis, and conversion. Prohep elevated the biosynthesis of the beneficial L-lysine, lipoic acid, pyrimidine, and palmitate. Prohep also elevated metabolic pathways related to energy utilization of lactic acid-producing bacteria (LAB) and acetate producers. Similarly, fecal acetate concentration was upregulated by Prohep. To sum up, Prohep demonstrated exceptional anti-tumorigenesis effects in the AOM/DSS model, which revealed its potential to develop into a novel CRC therapeutic in the future.}, } @article {pmid40890565, year = {2025}, author = {Ivanich, K and Yackzan, A and Flemister, A and Chang, YH and Xing, X and Chen, A and Yanckello, LM and Sun, M and Aware, C and Govindarajan, M and Kramer, S and Ericsson, A and Lin, AL}, title = {Ketogenic Diet Modulates Gut Microbiota-Brain Metabolite Axis in a Sex- and Genotype-Specific Manner in APOE4 Mice.}, journal = {Journal of neurochemistry}, volume = {169}, number = {9}, pages = {e70216}, doi = {10.1111/jnc.70216}, pmid = {40890565}, issn = {1471-4159}, support = {RF1AG062480/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet, Ketogenic/methods ; Female ; *Apolipoprotein E4/genetics ; Mice ; Male ; *Brain/metabolism ; *Sex Characteristics ; Genotype ; Mice, Inbred C57BL ; Apolipoprotein E3/genetics ; Mice, Transgenic ; }, abstract = {The apolipoprotein E4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), associated with early brain metabolic dysfunction and gut microbiome alterations. Targeting these early changes through dietary interventions may reduce AD risk in asymptomatic carriers. This study evaluated whether a ketogenic diet (KD) could reshape the gut microbiome and enhance key brain metabolite levels in young APOE4 mice, using APOE3 mice as a neutral-risk comparison. Male and female APOE3 and APOE4 mice were fed either a control diet or KD for 16 weeks, starting at 12 weeks of age. We used shotgun metagenomics and targeted brain metabolomics to identify microbe-metabolite signatures linked to neuroprotection. KD increased beneficial species such as Lactobacillus johnsonii and Lactobacillus reuteri while reducing pathogenic Bacteroides intestinalis. These microbial shifts correlated with improved brain metabolites related to mitochondrial function, neurotransmitter balance, redox homeostasis, and lipid metabolism. Notably, Lactobacillus species and B. intestinalis exhibited inverse correlations with key brain metabolite levels, suggesting their roles as both modulators and biomarkers of brain health. APOE4 females showed the greatest benefits, including restored microbiome diversity and normalization of brain metabolite levels. In contrast, APOE3 mice showed microbiome changes but limited brain metabolic responses. These findings highlight KD's potential to reprogram the gut-brain axis in a genotype- and sex-dependent manner, supporting its use as a precision nutrition strategy to reduce AD risk, particularly in asymptomatic female APOE4 carriers.}, } @article {pmid40890119, year = {2025}, author = {Yuan, B and Wang, S}, title = {Microbiome data integration via shared dictionary learning.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8147}, pmid = {40890119}, issn = {2041-1723}, support = {DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Colorectal Neoplasms/microbiology/therapy ; Machine Learning ; Immunotherapy ; Gastrointestinal Microbiome ; Computational Biology/methods ; }, abstract = {Data integration is a powerful tool for facilitating a comprehensive and generalizable understanding of microbial communities and their association with outcomes of interest. However, integrating data sets from different studies remains a challenging problem because of severe batch effects, unobserved confounding variables, and high heterogeneity across data sets. We propose a new data integration method called MetaDICT, which initially estimates the batch effects by weighting methods in causal inference literature and then refines the estimation via novel shared dictionary learning. Compared with existing methods, MetaDICT can better avoid the overcorrection of batch effects and preserve biological variation when there exist unobserved confounding variables, data sets are highly heterogeneous across studies, or the batch is completely confounded with some covariates. Furthermore, MetaDICT can generate comparable embedding at both taxa and sample levels that can be used to unravel the hidden structure of the integrated data and improve the integrative analysis. Applications to synthetic and real microbiome data sets demonstrate the robustness and effectiveness of MetaDICT in integrative analysis. Using MetaDICT, we characterize microbial interaction, identify generalizable microbial signatures, and enhance the accuracy of outcome prediction in two real integrative studies, including an integrative analysis of colorectal cancer metagenomics studies and a meta-analysis of immunotherapy microbiome studies.}, } @article {pmid40889848, year = {2026}, author = {Lin, X and Deng, C and Shu, Y and Li, S and Song, Y and Kong, H and Liang, Z and Liu, L and Rao, Y}, title = {Ecological presence and functional role of bacteriophages in fermented vegetables.}, journal = {Food microbiology}, volume = {133}, number = {}, pages = {104884}, doi = {10.1016/j.fm.2025.104884}, pmid = {40889848}, issn = {1095-9998}, mesh = {*Vegetables/microbiology/virology ; *Bacteriophages/genetics/isolation & purification/physiology/metabolism/classification ; Fermentation ; *Fermented Foods/virology/microbiology ; Microbiota ; *Bacteria/genetics/metabolism/virology/classification/isolation & purification ; Food Microbiology ; }, abstract = {Fermented vegetables are widely favored by consumers for their distinctive flavors and nutritional value, with their quality attributes being closely associated with microbiome dynamics. Recent advances in high-throughput sequencing technologies have revealed abundant bacteriophage resources within the fermented vegetable microbiome. These viral components significantly influence fermentation processes and product characteristics by modulating microbial community structure and function. However, research on optimizing vegetable fermentation processes through bacteriophage-mediated regulation remains in its nascent stage. This study systematically summarizes the compositional characteristics and dynamic patterns of microbial communities in fermented vegetables. We review the latest research progress on bacteriophage diversity and functional properties in fermented vegetables. Furthermore, by integrating multi-omics data, we provide insights into the complex interaction network among bacteriophages, host microbiota, and metabolic products. The results demonstrate that bacteriophages precisely regulate the fermentation process by mediating microbial community succession via lytic-lysogenic cycles and participating in the biosynthesis of key flavor compounds through encoded auxiliary metabolic genes. Finally, we sort out an integrated technical framework combining metagenomics and culturomics. This research provides novel insights into understanding the functional mechanisms of bacteriophages in fermented vegetables, offers a theoretical foundation for developing precision fermentation technologies based on bacteriophage regulation.}, } @article {pmid40889843, year = {2026}, author = {Ren, F and Liu, M and Tan, B}, title = {Mycobiota of highly-preserved and easily-spoiled soybean pastes-what are their roles?.}, journal = {Food microbiology}, volume = {133}, number = {}, pages = {104876}, doi = {10.1016/j.fm.2025.104876}, pmid = {40889843}, issn = {1095-9998}, mesh = {*Glycine max/microbiology ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Mycobiome ; Food Preservation ; Biodiversity ; }, abstract = {Effective preservation of fermented soybean pastes is critically dependent on their microbial communities. In this study, the fungal assemblages of highly-preserved (HP) and easily-spoiled (ES) soybean paste samples were analyzed and compared mainly with Illumina sequencing of both mycobiota ITS amplicon and metagenomic functional annotation. The results showed that fungal communities of two types soybean pastes were distinct and had different α-diversity and β-diversity characteristics. The phylum Ascomycota was predominant in all samples, with Candida, Aspergillus, and Penicillium being the most abundant genera. The HP group exhibited greater richness and diversity compared to ES samples, and the relative abundance of specific fungal taxa varied significantly between the two groups. Additionally, functional annotation revealed differences in metabolic categories, with HP samples having higher levels of functions related to amino acid transport and metabolism, cell cycle control, and signal transduction mechanisms. These results enhance the understanding of the fungal diversity and functional differences of soybean pastes, providing insights that could improve preservation methods, optimize production and storage processes, and ensure the quality of the products.}, } @article {pmid40888959, year = {2025}, author = {Rajan, RJ and Sathyanathan, R and Rajnish, KN}, title = {Metabarcoding-Based Seasonal Assessment of Airborne Microbial Communities in PM10 Samples from a Semi-Urban Region in Tamil Nadu, India.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {9}, pages = {1069}, pmid = {40888959}, issn = {1573-2959}, mesh = {India ; *Air Microbiology ; Seasons ; *Environmental Monitoring/methods ; *Microbiota ; *Air Pollutants/analysis ; *Particulate Matter/analysis ; Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; Air Pollution/statistics & numerical data ; }, abstract = {Airborne microbial communities show marked seasonal variability, with implications for both environmental processes and public health. In this study, metagenomic sequencing was applied to characterize airborne microbiota across four distinct seasons in India-winter (Sw), summer (Ss), southwest monsoon (Ssw), and northeast monsoon (Sne). Distinct shifts in dominant bacterial taxa were observed. Sne was dominated by Pseudomonas (42.3%) alongside sulfur-oxidizing Thiobacillus and Stenotrophomonas, likely influenced by lower temperatures and anthropogenic inputs. In Ss, Thiobacillus (72.9%) prevailed, followed by Pseudomonas (8.06%) and Sphingosinicella (6.68%), reflecting adaptation to arid, UV-intense conditions. Ssw featured Thiobacillus (58%) and Pseudomonas (18.5%) with additional plant-associated Lactobacillus and Clostridium, suggesting enhanced biogenic emissions. Sw was distinct for Enterococcus (21.9%) dominance and reduced Thiobacillus (16.2%), associated with high humidity and precipitation. Species richness followed the order Ssw > Sw > Ss > Sne, with the highest diversity during Ssw and Sw as indicated by Chao1, Fisher, Shannon, and Simpson indices. Kruskal-Wallis tests revealed no statistically significant differences in alpha diversity across seasons. Canonical Correspondence Analysis (CCA) highlighted strong seasonal structuring linked to environmental parameters such as temperature, humidity, and UV exposure. Dendrogram clustering showed greatest dissimilarity between Sne and Sw, while Ss and Ssw formed a closely related group. Ordination analyses (PCA, PCoA, NMDS) further confirmed seasonal distinctions. Seasonal variations in dominant bacterial taxa indicate potential public health risks in semi-urban tropical environments. Thiobacillus, prevalent in summer and the southwest monsoon, is generally non-pathogenic. In contrast, Pseudomonas species, abundant during the northeast monsoon and winter, are metabolically versatile, encompassing environmental strains and opportunistic pathogens known to cause respiratory and wound infections, especially in immunocompromised individuals. Winter also saw the presence of Enterococcus faecalis, a gut commensal and opportunistic pathogen linked to hospital-acquired infections and notable for multi-drug resistance. These seasonal shifts highlight varying exposure risks, emphasizing the need for public health attention to airborne microbial dynamics across different seasons.}, } @article {pmid40888678, year = {2025}, author = {Zhou, R and Ng, SK and Sung, JJY and Wong, SH and Goh, WWB}, title = {Detecting and mitigating doppelgänger bias in microbiome data: impacts on machine learning and disease classification.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2554196}, doi = {10.1080/19490976.2025.2554196}, pmid = {40888678}, issn = {1949-0984}, mesh = {Humans ; *Machine Learning ; Clostridium Infections/microbiology ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Obesity/microbiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Highly similar microbiome samples - so-called "doppelgänger pairs" - can distort analysis outcomes, yet are rarely addressed in microbiome studies. Here, we demonstrate that even a small proportion of such pairs (1-10% of samples) can substantially inflate machine learning performance across diverse disease cohorts including colorectal cancer (CRC), inflammatory bowel diseases (IBD), Clostridioides difficile infection (CDI), and obesity. Doppelgänger pairs also bias statistical tests and distort microbial network topology. In predictive models, classification accuracy was artificially boosted by 15-30% points across KNN, SVM, and Random Forest classifiers. In association testing, doppelgängers increased false-positive rates and decreased effect size stability; their removal reduced bootstrap variance by up to 28.3%. Moreover, the removal of doppelgängers yielded more stable networks. These effects were consistently observed across 16S, shotgun metagenomic, and simulated datasets. By accounting for highly similar samples, we reduce analytical noise and false discoveries, ultimately enabling more accurate and biologically meaningful microbiome insights.}, } @article {pmid40811873, year = {2025}, author = {Simpson, AM and Chase, AB and Rodríguez-Verdugo, A and Martiny, JB}, title = {Investigating bacterial evolution in nature with metagenomics.}, journal = {Current opinion in microbiology}, volume = {87}, number = {}, pages = {102654}, doi = {10.1016/j.mib.2025.102654}, pmid = {40811873}, issn = {1879-0364}, mesh = {*Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Genetic Variation ; *Evolution, Molecular ; *Biological Evolution ; }, abstract = {Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate in situ evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome's response to environmental change.}, } @article {pmid40789383, year = {2025}, author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK}, title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.}, journal = {Gene}, volume = {967}, number = {}, pages = {149720}, doi = {10.1016/j.gene.2025.149720}, pmid = {40789383}, issn = {1879-0038}, mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.}, } @article {pmid40749752, year = {2025}, author = {Von Tönnemann Pilati, G and da Silva Grisard, HB and Dorighello, RC and Filho, VB and Dahmer, M and Savi, BP and Elois, MA and Salles, GBC and Muniz, EC and Fongaro, G}, title = {Protocol for virome characterization in low-volume respiratory samples from broiler chickens.}, journal = {Journal of virological methods}, volume = {338}, number = {}, pages = {115233}, doi = {10.1016/j.jviromet.2025.115233}, pmid = {40749752}, issn = {1879-0984}, mesh = {Animals ; *Chickens/virology ; *Virome ; *Metagenomics/methods ; Brazil ; *Poultry Diseases/virology ; *Viruses/isolation & purification/genetics/classification ; Ultracentrifugation ; Trachea/virology ; Genome, Viral ; }, abstract = {The poultry industry is a major global source of animal protein but remains vulnerable to immunosuppressive viral infections that compromise bird health and productivity. This study evaluated five viral purification methods for metagenomic analysis of respiratory samples from broiler chickens in Santa Catarina, Brazil. Tracheal swabs from ten flocks (one per farm) were pooled, and 50 µL of a herpes simplex virus type 2 (HSV-2) and murine norovirus (MNV-1) mix was added as an internal positive control. The sample was centrifuged (2000 × g for 30 min), filtered (0.45 μm), and subjected to five purification methods. The filtrate was subjected to five different purification methods. Method 1 (M1) was based on nucleic acid direct genomic extraction of the supernatant. Method 2 (M2): a pre-treatment with DNase was used, followed by genomic extraction. Method 3 (M3) was performed using ultracentrifugation at 100,000 × g / 3 h at 4 °C, followed by genomic extraction. In Method 4 (M4), the sample was submitted to ultracentrifugation on a 25 % sucrose cushion at 100,000 × g / 3 h at 4 °C, followed by genomic extraction. Finally, in Method 5 (M5), the sample was ultracentrifuged on a 25 % sucrose cushion at 100,000 × g / 3 h at 4 °C, and the pellet was treated with DNase followed by genomic extraction. All genomic extractions were performed using the RNeasy Mini kit. Samples were reverse transcribed into cDNA and sequenced by the MiSeq Sequencing System. The efficiency of M1-5 was evaluated based on the yield of viral genetic material. All methodologies employed demonstrated varying rates of genome recovery from viruses identified in poultry production. Notable viruses included avian gyrovirus 2 (AGV-2), avian leukosis virus (ALV), and the avian endogenous retrovirus EAV-HP found within chicken genomes. However, M5 showed the best performance, recovering 9.32 % of viral sequences, 44 % of HSV-2, as internal viral control, 32 % of EAV-HP, 8 % of ALV, and 7 % of AGV-2. In conclusion, this study successfully evaluated and compared five distinct viral purification methods, contributing significantly to the characterization of avian viromes and enhancing comprehension of viral ecology.}, } @article {pmid40444400, year = {2025}, author = {Burdon, I and Bouras, G and Fenix, K and Yeo, K and Connell, J and Cooksley, C and Barry, E and Vreugde, S and Wormald, PJ and Psaltis, AJ}, title = {Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.}, journal = {International forum of allergy & rhinology}, volume = {15}, number = {9}, pages = {989-992}, pmid = {40444400}, issn = {2042-6984}, support = {//Garnett Passe and Rodney Williams Memorial Foundation/ ; APP1196832//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Paranasal Sinuses/microbiology ; RNA, Ribosomal, 16S/genetics ; *Sinusitis/microbiology ; }, abstract = {Long-read-metagenomic sequencing is the best method for analyzing the sinus microbiome. 16s-rRNA-sequencing (both long and short read) results in PCR amplification bias that significantly distorts the sinus microbiome.}, } @article {pmid40338446, year = {2025}, author = {Mei, S and Deng, Z and Meng, FY and Guo, QQ and Tao, HY and Zhang, L and Xi, C and Zhou, Q and Tian, XF}, title = {Sini Powder Alleviates Stress Response and Suppresses Hepatocellular Carcinoma Development by Restoring Gut Microbiota.}, journal = {Chinese journal of integrative medicine}, volume = {31}, number = {9}, pages = {802-811}, pmid = {40338446}, issn = {1993-0402}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver Neoplasms/drug therapy/pathology/microbiology ; *Carcinoma, Hepatocellular/drug therapy/pathology/microbiology ; Humans ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Powders ; Cell Proliferation/drug effects ; Mice ; Molecular Docking Simulation ; Cell Line, Tumor ; Hep G2 Cells ; Receptors, Adrenergic, beta-2/metabolism/genetics ; *Stress, Physiological/drug effects ; Cell Movement/drug effects ; Male ; Protein Interaction Maps/drug effects ; Cell Survival/drug effects ; Proto-Oncogene Mas ; }, abstract = {OBJECTIVES: To explore the underlying pharmacological mechanisms and its potential effects of Chinese medicine herbal formula Sini Powder (SNP) on hepatocellular carcinoma (HCC).

METHODS: The active components of SNP and their in vivo distribution were identified using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Construction of component-target-disease networks, protein-protein interaction network, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and molecular docking were employed to analyze the active components and anti-HCC mechanisms of SNP. Cell viability assay and wound healing assay were utilized to confirm the effect of SNP-containing serum (2.5%, 5.0%, 10%, 20%, and 40%), isoprenaline or propranolol (both 10, 100, and 1,000 µ mol/L) on proliferation and migration of HepG 2 or Huh7 cells. Meanwhile, the effect of isoprenaline or propranolol on the β 2 adrenergic receptor (ADRB2) mRNA expression on HepG2 cells were measured by real-time quantitative reverse transcription (RT-qPCR). Mice with subcutaneous tumors were either subjected to chronic restraint stress (CRS) followed by SNP administration (364 mg/mL) or directly treated with SNP (364 mg/mL). These two parallel experiments were performed to validate the effects of SNP on stress responses. Stress-related proteins and hormones were quantified using RT-qPCR, enzyme-linked immunosorbent assay, and immunohistochemistry. Metagenomic sequencing was performed to confirm the influence of SNP on the gut microbiota in the tumor-bearing CRS mice.

RESULTS: The distribution of the 12 active components of SNP was confirmed in various tissues and feces. Network pharmacology analysis confirmed the anti-HCC effects of the 5 active components. The potential anti-HCC mechanisms of SNP may involve the epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase Src (SRC) and signal transducer and activator of transcription 3 (STAT3) pathways. SNP-containing serum inhibited the proliferation of HepG2 and Huh7 cells at concentrations of 2.5% and 5.0%, respectively, after 24 h of treatment. Furthermore, SNP suppressed tumor progression in tumor-bearing mice exposed to CRS. SNP treatment also downregulated the expressions of stress-related proteins and pro-inflammatory cytokines, primarily by modulating the gut microbiota. Specifically, the abundance of Alistipes and Prevotella, which belong to the phylum Bacteroidetes, increased in the SNP-treated group, whereas Lachnospira, in the phylum Firmicutes, decreased.

CONCLUSION: SNP can combat HCC by alleviating stress responses through the regulation of gut microbiota.}, } @article {pmid40215391, year = {2025}, author = {Gómez, Á and Rodríguez-Largo, A and Pérez, E and García Freire, S and Hundehege, C and Berberich, E and Luján, L and Cortés, D}, title = {Clinicopathological progression and molecular characterization of intestinal dilatation syndrome in commercial brown layers.}, journal = {Veterinary pathology}, volume = {62}, number = {5}, pages = {740-747}, doi = {10.1177/03009858251331106}, pmid = {40215391}, issn = {1544-2217}, mesh = {Animals ; Female ; *Chickens ; *Poultry Diseases/pathology/microbiology ; Retrospective Studies ; Dilatation, Pathologic/veterinary/pathology ; Jejunum/pathology/microbiology ; *Intestinal Diseases/veterinary/pathology/microbiology ; Proventriculus/pathology/microbiology ; Gastrointestinal Microbiome ; }, abstract = {Intestinal dilatation syndrome (IDS) is a poorly described condition affecting layers and breeder hens globally. Its prevalence is increasing, particularly in free-range systems, but the cause remains unknown. This retrospective study examined 35 hens from 3 flocks: free-range flock A (n = 20) and enriched-caged flock B (n = 5), both affected by IDS, and enriched-caged flock C (n = 10), with no history of IDS. Clinicopathological studies were performed on these hens, and metagenomic analysis was conducted on the proventriculus and jejunum of hens from flock A (n = 2) and flock C (n = 2). Based on clinical signs and lesions, 3 progressive stages of IDS were identified. In the first stage, although hens were without clinical signs, proventricular dilatation and lymphoplasmacytic and heterophilic jejunitis and duodenitis were observed. The second stage was marked by cachexia, pale and small combs and wattles, and severe egg production drop. Jejunal dilatation was observed, with microscopic evidence of necrotic, lymphoplasmacytic and heterophilic jejunitis; ganglioneuritis; and mineralization of the jejunal nervous plexuses and subserosal ganglia. In the third stage, spontaneous death occurred due to jejunal volvulus and vascular involvement. Affected hens (stage 2) also exhibited elevated cloacal temperatures (>0.9°C) and marked heterophilia. Metagenomic analysis identified sequences consistent with Megrivirus C in IDS-affected hens and a disruption of the gut microbiota, with increased abundance of Fusobacterium mortiferum and Megamonas funiformis. In conclusion, this study describes in detail the clinicopathological progression of the IDS and suggests that Megrivirus C, in combination with opportunistic intestinal bacteria, could play a role in the pathogenesis of this disease.}, } @article {pmid40886152, year = {2025}, author = {Zemmel, ZM and Fan, X and Yu, Y and Markiewicz, E and Tsai, HM and Lu, L and Little, JC and Ramaswamy, R and Andrews, B and Claud, EC and Lu, J}, title = {Early-life gut microbiome maturity regulates blood-brain barrier and cognitive development.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2551879}, doi = {10.1080/19490976.2025.2551879}, pmid = {40886152}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Blood-Brain Barrier/metabolism/physiology/growth & development ; Mice ; Female ; Humans ; *Cognition/physiology ; Pregnancy ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Brain/growth & development/metabolism ; Male ; Germ-Free Life ; }, abstract = {The gut microbiome is an emerging factor in the neurobiology of disease. Blood-brain barrier (BBB) integrity is essential for proper brain function. However, the role the initial microbiome plays in BBB and brain development is unclear. In this study, we colonized germ-free pregnant mice with human full-term- or preterm-infant-derived gut microbiota, thereby establishing these communities in the resulting offspring. We discovered that mice harboring a full-term-associated microbiome exhibited stronger memory and learning capabilities and dramatically decreased early-life BBB permeability when compared to those with a prematurity-associated microbiome. Whole-brain single-cell RNA sequencing revealed downregulation of synaptic signaling genes in BBB cell types of mice with the prematurity-associated microbiome, indicating that microbiome maturity influences BBB transcriptional programs that support cognitive development. Comprehensive metagenomics and metabolomics uncovered bacterial populations and genomic pathways corresponding with decreased levels of circulating long-chain acylcarnitines and lysophosphatidylcholines in mice with the full-term-associated microbiome. Our findings highlight the microbiome as a therapeutic target for improving long-term neurodevelopmental outcomes due to its effect on the early-life BBB.}, } @article {pmid40885910, year = {2025}, author = {Huang, W and Chai, Y and Li, X and Zhang, Q and Yan, Z and Wang, Y and Tao, X and Zhang, J and Qiu, F}, title = {Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {567}, pmid = {40885910}, issn = {1471-2180}, support = {2018YFA0108601//Clinical research on intracerebral precision transplantation of neural stem cells for stroke treatment/ ; L255012//The Huairou Innovation Joint Fund Project of Beijing Natural Science Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Infarction/microbiology/blood/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; Female ; Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Tandem Mass Spectrometry ; Adult ; Chromatography, High Pressure Liquid ; }, abstract = {Cerebral infarction, a cerebrovascular disorder, is characterized by the sudden onset of neurological deficits and clinical symptoms. It ranks among the leading causes of death and severe disability worldwide. The etiology of cerebral infarction is multifaceted, with common risk factors including dietary patterns, smoking, hypertension, and diabetes mellitus. In recent years, the role of the gut microbiota in systemic immunity and tumorigenesis has been intensively explored, thrusting the research on the gut-brain axis into the spotlight. However, there is a lack of literature investigating the relationship between the gut microbiota and blood metabolites in cerebral infarction. In this study, we employed 16S rRNA analysis and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) for a comprehensive metagenomic and metabolomic analysis of fecal samples from cerebral infarction patients and the general population. Our results revealed a significant correlation between the gut microbiome and serum metabolites, highlighting the impact of the microbiome on metabolic pathways. Specifically, we found that 35 gut microbiome taxa, such as Actinobacteriota and Peptostreptococcales-Tissierellales, were significantly enriched in the control group (N group). Through Linear Discriminant Analysis Effect Size (LEfSe) analysis, 72 taxa showed significant differences between cerebral infarction patients and healthy individuals. Among them, 22 key taxa were identified as microbial biomarkers for differentiating patients from healthy controls. These findings suggest that variations in the microbiome and metabolites could potentially serve as biomarkers for future diagnostic and therapeutic strategies in cerebral infarction.}, } @article {pmid40885737, year = {2025}, author = {Chatzigiannidou, I and Johansen, PL and Dehli, RK and Moll, JM and Eriksen, C and Myers, PN and Roager, HM and Yang, L and Stokholm, J and Sørensen, SJ and Krogfelt, KA and Laursen, MF and Trivedi, U and Scheynius, A and Kristiansen, K and Mie, A and Alm, J and Brix, S}, title = {Temporal dynamics and microbial interactions shaping the gut resistome in early infancy.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8139}, pmid = {40885737}, issn = {2041-1723}, support = {2012-3011//Vetenskapsrådet (Swedish Research Council)/ ; 0171-00006B//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; 4203-00005B//Innovationsfonden (Innovation Fund Denmark)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Escherichia coli/genetics/drug effects/growth & development ; Female ; Infant, Newborn ; Bifidobacterium/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Microbial Interactions/genetics ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics ; Male ; }, abstract = {Despite the critical role of the gut resistome in spreading of antimicrobial resistance (AMR), strategies to reduce the abundance of antibiotic resistance genes (ARGs) during microbiota development in infancy remain underexplored. Using longitudinal quantitative metagenomic data, we here show that ARGs are present in the gut microbiota from the first week of life, with a peak in absolute ARG abundance and richness at 6 months. Delivery mode significantly affects early ARG dynamics, and vaginally delivered infants exhibit higher ARG abundance due to maternal transmission of Escherichia coli strains harbouring extensive resistance repertoires. The abundance of E. coli and other ARG-rich taxa inversely correlates with aromatic lactic acid-producing bifidobacteria, and aromatic lactic acids strongly inhibit the in vitro growth of E. coli and other opportunistic ARG-rich taxa. Our results highlight temporal and critical microbial interactions shaping the gut resistome in early infancy, pointing to potential interventions to curb AMR during this vulnerable developmental window by promoting colonization of aromatic lactic acid-producing bifidobacteria.}, } @article {pmid40885659, year = {2025}, author = {Klier, KM and Anantharaman, K}, title = {An updated view of metabolic handoffs in microbiomes.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.07.009}, pmid = {40885659}, issn = {1878-4380}, abstract = {From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and interactions that shape these communities, however, constrains efforts to culture, investigate, and harness their potential. Further, these knowledge gaps restrict the ability to predict microbial responses to broader biodiversity declines and global change. Among the numerous types of microbial interactions, metabolite exchanges, or 'metabolic handoffs', are a well-documented phenomenon. Recent methodological advances have uncovered a broader spectrum of metabolic handoffs than previously appreciated. Varying in both mechanism and ecological role, metabolic handoffs influence diverse natural environments. In this review, we define two major types of metabolic handoffs, examine their potential drivers and benefits, and highlight emerging research that underscores their widespread occurrence and importance in complex microbial ecosystems.}, } @article {pmid40884577, year = {2025}, author = {Kumar, V and Sandil, S and Verma, P and Ameen, F}, title = {Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system.}, journal = {Archives of microbiology}, volume = {207}, number = {10}, pages = {247}, pmid = {40884577}, issn = {1432-072X}, support = {ORF-2025-364//The authors extend their appreciation to the ongoing research funding program, (ORF-2025-364), King Saud University, Riyadh, Saudi Arabia./ ; }, mesh = {*Sewage/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Microbiota ; Metals, Heavy/analysis ; Industrial Waste/analysis ; }, abstract = {This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC-MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that Proteobacteria was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as Bacteriodetes, Acidobacteria, Planctomycetes, Chlorolfexi, Actinobacteria, and Verrucomicrobia were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.}, } @article {pmid40883413, year = {2025}, author = {Manzoor, M and Pussinen, PJ and Saarela, RKT and Hiltunen, K and Mäntylä, P}, title = {Metagenomic analysis of the denture-associated oral microbiome in patients with denture stomatitis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31913}, pmid = {40883413}, issn = {2045-2322}, support = {1340750//Research Council of Finland/ ; }, mesh = {Humans ; Female ; Male ; *Stomatitis, Denture/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged, 80 and over ; Aged ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Dentures/microbiology ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Denture stomatitis (DS) is an inflammatory condition that affect denture wearers and is characterized by erythema of the mucosa opposing the denture. DS is often associated with oral microbiome dysbiosis. We used shotgun metagenomics to investigate the association between the denture-associated oral microbiome (DAOM) and DS in older adults living in long-term care facilities. We included participants with DS (n = 28) and age-and sex-matched removable denture wearers without signs of DS (n = 28). Clinical oral examinations were performed, and demographic and medical data were obtained from medical records. Median (interquartile range) age of participants was 88 (9) years; 75% were females. Beta diversity differed between the DS and non-DS groups (Bray-Curtis dissimilarity, p = 0.01; Jaccard index, p = 0.004). Two phyla, nine genera, and 15 species differed significantly between groups, with the genera Candida and Scardovia, and species Candida albicans, Aggregatibacter actinomycetemcomitans, and Scardovia inopinata being enriched in DS. Network analysis revealed strongly interconnected microbial communities and more prominent bacterial-fungal co-occurrence in DS than in non-DS. These findings indicate that DS is associated with significant alterations in the DAOM, which may contribute to inflammation. Microbiome-targeted strategies are needed for the management of DS.}, } @article {pmid40883308, year = {2025}, author = {Chen, T and Xiong, Y and Zhang, J and Zhang, Q and Wu, J and Xu, N and Liu, T}, title = {Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {178}, pmid = {40883308}, issn = {2055-5008}, support = {20220808011114001//Shenzhen Natural Science Fund/ ; }, mesh = {*Lakes/microbiology/virology ; *Cyanobacteria/virology/growth & development ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; China ; Biodiversity ; Eutrophication ; *Harmful Algal Bloom ; *Virome ; }, abstract = {Harmful cyanobacterial blooms pose severe threats to aquatic ecosystems. Bloom-forming cyanobacteria form cyanobacterial aggregates (CAs) that create a phycosphere supporting diverse microbial interactions. Here, longitudinal metagenomics and metatranscriptomics were employed to explore the temporal variation of CA-attached viral communities throughout cyanobacterial blooms in Lake Taihu. Viral communities, represented by 5613 viral operational taxonomic units, showed increased relative abundance (RPKM) with the expansion of bloom areas. Among 1791 virus‒host linkages, host shifts followed the succession of two dominant cyanobacterial genera, Microcystis and Dolichospermum. Viruses demonstrated high virus‒host abundance ratios within all host genera and showed elevated transcriptional activities infecting Dolichospermum during the late bloom stage. Viruses featured high microdiversity and positively selected replication-associated genes in response to abundant host genera and variable trophic status. This study uncovered diverse active viral auxiliary metabolism associated with photosynthesis, biochemical cycling, and DNA biosynthesis, and highlighted the significant role of phycosphere-associated viruses during cyanobacterial blooms.}, } @article {pmid40883297, year = {2025}, author = {Chen, XP and Zhu, D and Liu, SY and Sun, MM and Ye, M and Wang, L and Lin, D and Zhang, TL and Rillig, MC and Zhu, YG}, title = {Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8098}, pmid = {40883297}, issn = {2041-1723}, support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; *Microbiota/genetics ; *Ecosystem ; *Virome/genetics ; Metagenomics/methods ; Soil Microbiology ; Bacteria/metabolism/genetics/virology ; }, abstract = {Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their functions in the plastisphere. Here, we investigate the composition and functional profile of plastisphere viral communities through microcosm experiments combined with global plastisphere metagenomics data. We find that the plastisphere recruits a distinct viral community with 86.9% novel viral operational taxonomic units compared to control substrates. The plastisphere viral community modulates host methane metabolism through auxiliary metabolic genes and distinctive interactions with hosts. These auxiliary metabolic genes for methane cycling are prevalent in global plastisphere viral communities. Notably, the plastisphere microbiome adopts the life history strategy of copiotrophs in the nutrient-poor water environment, making the water plastisphere a potential hot spot for methane emission compared to the soil plastisphere. Our phage transplantation experiments reveal that lysogenic viruses significantly contribute to enhancing the methanogenic capacity of microorganisms and promoting methane emission of the water plastisphere. Overall, we decipher the role of viruses in the plastisphere and reinforce the necessity of incorporating viral contributions when assessing the effects of plastisphere communities on global biogeochemical cycles.}, } @article {pmid40878918, year = {2025}, author = {Liu, X and Xie, Y and Yang, S and Jiang, C and Shang, K and Luo, J and Zhang, L and Hu, G and Liu, Q and Yue, B and Fan, Z and He, Z and Li, J}, title = {Multi-omics investigation of spontaneous T2DM macaque emphasizes gut microbiota could up-regulate the absorption of excess palmitic acid in the T2DM progression.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {40878918}, issn = {2050-084X}, support = {2021YJ0136//Science and Technology Foundation of Sichuan Province/ ; 32171607//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology/pathology/metabolism ; *Palmitic Acid/metabolism ; Macaca mulatta ; Mice ; Disease Models, Animal ; Male ; Gene Expression Profiling ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Multiomics ; }, abstract = {Although gut microbiota and lipid metabolites have been suggested to be closely associated with type 2 diabetes mellitus (T2DM), the interactions between gut microbiota, lipid metabolites, and the host in T2DM development remains unclear. Rhesus macaques may be the best animal model to investigate these relationships given their spontaneous development of T2DM. We identified eight spontaneous T2DM macaques and conducted a comprehensive study investigating the relationships using multi-omics sequencing technology. Our results from 16 S rRNA, metagenome, metabolome, and transcriptome analyses identified that gut microbiota imbalance, tryptophan metabolism and fatty acid β oxidation disorders, long-chain fatty acid (LCFA) accumulation, and inflammation occurred in T2DM macaques. We verified the accumulation of palmitic acid (PA) and activation of inflammation in T2DM macaques. Importantly, mice transplanted with spontaneous T2DM macaque fecal microbiota and fed a high PA diet developed prediabetes within 120 days. We determined that gut microbiota mediated the absorption of excess PA in the ileum, resulting in the accumulation of PA in the serum, consequently leading to T2DM in mice. In particular, we demonstrated that the specific microbiota composition was probably involved in the process. This study provides new insight into interactions between microbiota and metabolites and confirms causative effect of gut microbiota on T2DM development.}, } @article {pmid40877975, year = {2025}, author = {Xu, L and Jiao, JY and Ling, C and Du, RB and Wu, Q and Xu, Y and Li, WJ}, title = {Mobilome-mediated transcriptional activation of biosynthetic gene clusters and its impact on strain competitiveness in food fermentation microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {191}, pmid = {40877975}, issn = {2049-2618}, support = {32172175//National Natural Science Foundation of China/ ; No. 111-2-06//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, mesh = {Fermentation ; *Microbiota/genetics ; *Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism ; *Transcriptional Activation ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Interspersed Repetitive Sequences ; *Food Microbiology ; Firmicutes/genetics ; *Fermented Foods/microbiology ; Microbial Interactions/genetics ; }, abstract = {BACKGROUND: Microbial interactions are critical for maintaining the stability of food fermentation microbiomes, and mobile genetic elements (MGEs) significantly influence these interactions by horizontal gene transfer events. Although MGEs are known to facilitate horizontal gene transfer, their distribution among microorganisms and specific effects on microbial interactions remain poorly understood.

RESULTS: We analyzed 590 metagenomic and 42 metatranscriptomic samples from food fermentations, recovering 1133 metagenome-assembled genomes (MAGs). Our analysis revealed that MGEs were widely distributed in food fermentation microbiomes, with higher occurrence rates in Firmicutes (Bacillota: 0.71 ~ 11.85%) and Proteobacteria (Pseudomonadota: 0.47 ~ 11.05%). MGEs tended to be located adjacent to functional genes, particularly biosynthetic gene clusters (BGCs), with co-occurrence rates ranging from 9.41 to 23.99%. Furthermore, the transcriptional activity of BGCs was significantly correlated with the number of MGEs that were co-located with BGCs, which might enhance the competitiveness of strains. Variability in the diversity of MGEs that were co-located with BGCs was also evident at the strain level. Using Lactiplantibacillus plantarum as a case, we revealed that the strain-level differences in MGEs that were co-located with BGCs are positively correlated with the transcription of BGCs and competitiveness of strains within the species.

CONCLUSIONS: This study highlighted the role of MGEs in enhancing transcription of BGCs and facilitating strain competitiveness, providing new insights into how MGEs enhance the adaptability of microbial communities. Video Abstract.}, } @article {pmid40811063, year = {2025}, author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, AD and Lieberman, TD}, title = {Intraspecies associations from strain-rich metagenome samples.}, journal = {Cell reports}, volume = {44}, number = {8}, pages = {116134}, doi = {10.1016/j.celrep.2025.116134}, pmid = {40811063}, issn = {2211-1247}, support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Metagenome/genetics ; Phylogeny ; *Microbiota/genetics ; Female ; *Metagenomics/methods ; Vagina/microbiology ; Skin/microbiology ; }, abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference database approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based framework to quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we find clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will enable strain-level insights from accumulating metagenomic data.}, } @article {pmid40793873, year = {2025}, author = {Manning, S and Hackney, E and Dunneram, Y and Hull, MA and Mitra, S and Stewart, CJ and Louca, P and Meader, N and Sharp, L and Rees, C}, title = {Systematic Review: The Relationship Between the Faecal Microbiome and Colorectal Neoplasia in Shotgun Metagenomic Studies.}, journal = {Alimentary pharmacology & therapeutics}, volume = {62}, number = {6}, pages = {568-584}, pmid = {40793873}, issn = {1365-2036}, support = {//Guts UK/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Reproducibility of Results ; }, abstract = {BACKGROUND: The human gut microbiome is of academic and clinical interest. Associations between certain organisms and colorectal neoplasia have been reported, but findings have limited reproducibility in different populations.

METHODS: We performed a systematic review of whole metagenome shotgun sequencing studies using faecal samples from patients with colorectal neoplasia and control populations. Searches were performed on 30th June 2023. We identified 26 studies, reporting on 22 study populations (13 from Asia, five from Europe and four from North America). Study size ranged from 14 to 971 individuals (mean 170).

RESULTS: Some reproducible data were identified, such as the significant enrichment of Fusobacterium nucleatum and Parvimonas micra in colorectal cancer patients compared to controls (in 10 and nine studies, respectively). However, 21 out of 26 studies scored poorly on quality appraisal, specifically surrounding selection of cases and controls. Definitions of controls varied; some studies used individuals with normal endoscopic investigations, some used 'healthy' individuals where no colonoscopy was performed, and one used those with non-neoplastic findings (haemorrhoids). There was even less reproducibility of data in studies where individuals with colorectal polyps were compared to controls, possibly because of heterogeneity in these patient groupings as a variety of definitions for 'polyp cases' were used.

CONCLUSIONS: Heterogeneity and potential for bias indicates that findings should be interpreted with caution. Standardised protocols to ensure robust methodology and allow pooling of large-scale data are required before these findings can be used in clinical practice (PROSPERO: CRD42023431977).}, } @article {pmid40694475, year = {2025}, author = {Pfeifer, E and d'Humières, C and Lamy-Besnier, Q and Oñate, FP and Denisé, R and Dion, S and Condamine, B and Touchon, M and Ma, L and Burdet, C and Mentré, F and Denamur, E and Rocha, EPC and , }, title = {Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages.}, journal = {Cell reports}, volume = {44}, number = {8}, pages = {116020}, doi = {10.1016/j.celrep.2025.116020}, pmid = {40694475}, issn = {2211-1247}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Bacteriophages/drug effects/pathogenicity/genetics ; *Anti-Bacterial Agents/pharmacology ; Female ; Male ; Adult ; Virulence/drug effects ; Cephalosporins/pharmacology ; }, abstract = {Antibiotic use disrupts the gut microbiota, posing risks of long-term health issues and resistance. To study its impact on gut phages, we followed 22 healthy individuals 2 weeks before and up to 6 months after a 3-day course of 3[rd]-generation cephalosporins. Our results show that gut phages rarely encode antibiotic resistance genes and are mostly temperate, including many phage plasmids. Furthermore, phage populations remain individual-specific even after microbiome perturbation. Yet, we report a 20% decline in phage diversity the day after treatment, alongside blooms of a few, mostly virulent, phages. We suggest that some of these phages contribute to the recovery of bacterial diversity via "kill-the-winner" dynamics. This is supported by (temporarily) dominant phages targeting Parabacteroides distasonis, a bacterium that thrives post-treatment only in the absence of these phages. Our findings suggest gut phages are crucial to the microbiome response to antibiotics, aiding the restoration of balance and diversity.}, } @article {pmid40877311, year = {2025}, author = {Wilson, BC and Zuppi, M and Derraik, JGB and Albert, BB and Tweedie-Cullen, RY and Leong, KSW and Beck, KL and Vatanen, T and O'Sullivan, JM and Cutfield, WS and , }, title = {Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7786}, pmid = {40877311}, issn = {2041-1723}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; Male ; Female ; Follow-Up Studies ; Double-Blind Method ; *Pediatric Obesity/therapy ; Treatment Outcome ; Body Composition ; Body Mass Index ; Gastrointestinal Microbiome ; *Obesity/therapy ; Metabolic Syndrome/therapy ; Feces/microbiology ; }, abstract = {Faecal microbiota transplantation (FMT) has been explored as a potential treatment for obesity, but its long-term effects on metabolic health remain unclear. Here, we report 4-year follow-up findings from a double-blind, randomised, placebo-controlled trial assessing FMT in adolescents with obesity (ACTRN12615001351505, Australian New Zealand Clinical Trials Registry). This unblinded follow-up study evaluated 63% (55/87) of the original participants (27 FMT, 28 placebo). There was no difference in BMI between the two groups, after adjusting for sex, age, diet, and physical activity (-3.6 kg/m[2], p = 0.095). However, FMT recipients showed clinical improvements in body composition and metabolic health compared to the placebo group. Specifically, FMT recipients had smaller waist circumference (-10.0 cm, p = 0.026), total body fat (-4.8%, p = 0.024), metabolic syndrome severity score (-0.58, p = 0.003), and systemic inflammation (-68% hs-CRP, p = 0.002) and higher levels of HDL cholesterol (0.16 mmol/L, p = 0.037). No group differences were observed in glucose markers, or other lipid parameters. Shotgun metagenomic sequencing revealed sustained long-term alterations in gut microbiome richness, composition and functional capacity, with persistence of donor-derived bacterial and bacteriophage strains. These findings highlight the potential relevance of FMT as a microbiome-augmenting intervention for obesity management and metabolic health, warranting further investigation.}, } @article {pmid40874749, year = {2025}, author = {Gao, J and Han, W and Jiang, X and Xi, Y and Chen, Y and Huang, S and Huang, X and Zhang, Y and Zhang, T and Zhang, M and Zhang, W and Ni, B}, title = {Unexplored viral diversity in Siberian cranes and wild geese: metagenomic insights from a global wintering haven.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075625}, doi = {10.1128/msystems.00756-25}, pmid = {40874749}, issn = {2379-5077}, abstract = {Migratory birds are critical global carriers and vectors of various viruses, potentially driving the mutation and transmission of novel pathogens, especially zoonotic viruses. Despite advancements in sequencing technologies, the viral diversity in wintering Siberian cranes (Leucogeranus leucogeranus) and wild geese (Anser spp.) remains poorly understood. In this study, we conducted a viral metagenomic survey of fecal samples from 320 Siberian cranes and wild geese wintering in Poyang Lake, China. Through this approach, we identified 183 novel viruses associated with known and putative vertebrate-infecting viruses, including a novel coronavirus, parvoviruses, picornaviruses, picobirnaviruses, anelloviruses, and CRESS-DNA viruses. Furthermore, we detected evidence of cross-species transmission and identified viruses with zoonotic potential, such as picobirnaviruses and picornaviruses. These findings highlight the significant public health risks posed by migratory birds and provide new insights into the viral diversity within these populations, contributing to a better understanding of their role in viral evolution and transmission.IMPORTANCEUnderstanding the diversity of enteroviruses in Siberian cranes and geese is essential for biodiversity conservation and ecosystem stability. As migratory birds, these species play key roles in ecological networks while carrying intestinal viruses that may spread along migration routes, which could pose potential risks to wildlife, poultry, and human health. This study systematically analyzed enterovirus diversity and the genetic characteristics of novel viruses in wintering Siberian cranes and geese at Poyang Lake using metagenomic sequencing. We identified viral sequences distantly related to known viruses and those with potential cross-species transmission risks. These findings highlight the diversity of migratory bird viruses and their public health implications, providing data to evaluate transmission risks and monitor emerging threats, supporting strategies for wildlife conservation and disease prevention.}, } @article {pmid40873785, year = {2025}, author = {Bei, Q and Williams, NLR and Furtado, LE and Blasi, DD and Williams, J and Brotas, V and Tarran, G and Rees, AP and Bowler, C and Fuhrman, JA}, title = {Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf131}, pmid = {40873785}, issn = {2730-6151}, abstract = {High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater. We applied this method to surface waters collected across 50°N to 40°S during the 29[th] Atlantic Meridional Transect. Using the single-copy recA gene, we estimated an average bacterial abundance of 1.0 × 10[9] haploid genome equivalents per liter. Leveraging a recent report that the psbO gene is typically single-copy in phytoplankton, we also quantified eukaryotic phytoplankton. Metagenomic estimates closely aligned with flow cytometry data for cyanobacteria (slope = 1.03, Pearson's r = 0.89) and eukaryotic phytoplankton (slope = 0.72, Pearson's r = 0.84). Compared to flow cytometry, taxonomic resolution for nano- and picoeukaryotes was greatly improved. Estimates for diatoms, dinoflagellates, and Trichodesmium were considerably higher than microscopy counts, likely reflecting microscopy undercounts and potential ploidy variation. These findings highlight the value of absolute quantification by metagenomics and offer a robust framework for quantitative assessments in microbial oceanography.}, } @article {pmid40872269, year = {2025}, author = {Britto Martins de Oliveira, J and Barbieri, M and Corrêa-Junior, D and Schmitt, M and Santos, LLR and Bahia, AC and Parente, CET and Frases, S}, title = {Urban Mangroves Under Threat: Metagenomic Analysis Reveals a Surge in Human and Plant Pathogenic Fungi.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/pathogens14080759}, pmid = {40872269}, issn = {2076-0817}, support = {CNE//FAPERJ/ ; 001//CAPES/ ; BP//CNPQ/ ; }, mesh = {*Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification ; Humans ; *Wetlands ; Ecosystem ; Biodiversity ; Mycobiome ; Geologic Sediments/microbiology ; }, abstract = {Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness-28% lower than expected for similar ecosystems-likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments.}, } @article {pmid40872213, year = {2025}, author = {Raza, A and Ling, SJ and Wei, YL and Bahadur, S and Ren, MX}, title = {Facilitation in the Dry Season: Species Interactions Between a Limestone-Endemic Plant and Moss Altered by Precipitation Dynamics.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/plants14162588}, pmid = {40872213}, issn = {2223-7747}, support = {ZDYF2023RDYL01//Hainan Tropical Rainforest Conservation/ ; 42371054//National Natural Science Foundation of China/ ; }, abstract = {Plant-to-plant interactions are essential for structuring plant communities and supporting adaptation in nutrient-poor, seasonally dry environments. This study examined the interactions between moss Leucobryum aduncum Dozy & Molk and Oreocharis hainanensis by analyzing microbial communities and physicochemical parameters across various sample types. These included soil [bare (B), O. hainanensis (O), moss (M), and moss + O. hainanensis (MO)], rhizosphere soil [O. hainanensis (ORS), moss (MRS), and moss + O. hainanensis (MORS)], and root [O. hainanensis (OHR), moss (MR), and moss + O. hainanensis (MOR)] using metagenomics sequencing across dry and wet seasons in limestone habitats on Hainan Island. During the dry season, combined plant samples MOR, MO, and MORS showed higher nutrients, supported by microbes that enhance nutrient turnover, which may indicate facilitation. Conversely, during the wet season, increased moisture leads to decreased nutrient levels and microbial communities shift, associated with slower nutrient turnover in combined plant samples, which may reflect competition. According to KEGG analysis, an increase in oxidative phosphorylation and ABC transporters in the dry season supported the facilitative interaction, while quorum sensing and two-component systems supported the competitive interaction in the wet season. These findings show how shifts between facilitation and competition arise from seasonal conditions and microbes in the limestone ecosystem.}, } @article {pmid40872157, year = {2025}, author = {Nityagovsky, NN and Ananev, AA and Suprun, AR and Dneprovskaya, AA and Kiselev, KV and Aleynova, OA}, title = {Endophytic Bacterial and Fungal Communities of Spruce Picea jezoensis in the Russian Far East.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {16}, pages = {}, doi = {10.3390/plants14162534}, pmid = {40872157}, issn = {2223-7747}, support = {22-74-10001//Russian Science Foundation/ ; 124012200181-4//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {A wide range of microorganisms, including endophytes, frequently interact with forest trees. The role of endophytes in industrial conifers has not been fully investigated. The Yezo spruce Picea jezoensis is widely used for logging in Russia and Japan. In this work, the endophytic communities of bacteria and fungi in healthy needles, branches, and fresh wood of P. jezoensis from Primorsky Territory were analyzed using metagenomic analysis. The results indicate that the diversity of endophytic communities in P. jezoensis is predominantly influenced by the specific tree parts (for both bacteria and fungi) and by different tree specimens (for fungi). The most abundant bacterial classes were Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. Functional analysis of KEGG orthologs (KOs) in endophytic bacterial community using PICRUSt2 and the PLaBAse PGPT ontology revealed that 59.5% of the 8653 KOs were associated with plant growth-promoting traits (PGPTs), mainly, colonization, stress protection, bio-fertilization, bio-remediation, vitamin production, and competition. Metagenomic analysis identified a high abundance of the genera Pseudomonas and Methylobacterium-Methylorubrum in P. jezoensis, which are known for their potential growth-promoting activity in other coniferous species. The dominant fungal classes in P. jezoensis were Dothideomycetes, Sordariomycetes, and Eurotiomycetes. Notably, the genus Penicillium showed a pronounced increase in relative abundance within the fresh wood and needles of Yezo spruce, while Aspergillus displayed elevated abundance specifically in the fresh wood. It is known that some of these fungi exhibit antagonistic activity against phytopathogenic fungi. Thus, our study describes endophytic communities of the Yezo spruce and provides a basis for the production of biologicals with potential applications in forestry and agriculture.}, } @article {pmid40871697, year = {2025}, author = {Wang, B and Peters-Samuelson, BA and Luo, K and Cordero, C and Perreira, KM and Pirzada, A and Daviglus, ML and Li, Y and Kaplan, RC and Burk, RD and Qi, Q}, title = {Interplays of ADH1B Genotype, Alcohol Consumption, and Gut Microbiota in Relation to Insulin Resistance.}, journal = {Nutrients}, volume = {17}, number = {16}, pages = {}, doi = {10.3390/nu17162669}, pmid = {40871697}, issn = {2072-6643}, support = {R01-DK119268/DK/NIDDK NIH HHS/United States ; R01-DK126698/DK/NIDDK NIH HHS/United States ; R01-DK120870/DK/NIDDK NIH HHS/United States ; P30DK111022/DK/NIDDK NIH HHS/United States ; R01-MD011389/MD/NIMHD NIH HHS/United States ; UM1-HG008898/HG/NHGRI NIH HHS/United States ; R01-HL060712//National Heart Lung and Blood Institute/ ; R01-HL140976//National Heart Lung and Blood Institute/ ; R01-HL136266//National Heart Lung and Blood Institute/ ; }, mesh = {Humans ; *Alcohol Dehydrogenase/genetics ; *Insulin Resistance/genetics ; *Gastrointestinal Microbiome/genetics ; *Alcohol Drinking/genetics ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; *Genotype ; Adult ; Feces/microbiology ; Longitudinal Studies ; }, abstract = {BACKGROUND/OBJECTIVE: Alcohol consumption has been linked to alterations in gut microbiota and insulin resistance. The alcohol dehydrogenase 1B (ADH1B) gene plays a crucial role in alcohol catabolism, where rs1229984 variant carriers (CT/TT) catabolize ethanol at an 80-fold faster rate than non-carriers (CC). This study investigates the relationships between ADH1B gene rs1229984 mutation, alcohol consumption, gut microbiota, and insulin resistance.

METHODS: We performed cross-sectional analysis on fecal metagenomic sequencing data from diabetes-free participants in a longitudinal cohort of the Hispanic Community Health Study/Study of Latinos. We used Analysis of Composition of Microbiomes to identify gut microbial species associated with alcohol consumption in non-carriers (n = 1399) and carriers (n = 193). We constructed genotype-specific gut microbiome scores (GMSs) based on the identified species associated with alcohol consumption to examine how gut microbiota may influence the relationship between alcohol consumption and insulin resistance across ADH1B genotypes. Insulin resistance was defined as Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) > 2.5.

RESULTS: Distinct microbial species associated with alcohol consumption were identified in non-carriers (54 species) and carriers (16 species). In non-carriers, the genotype-specific GMS modified the relationship between alcohol consumption and insulin resistance (Pinteraction = 0.011). The odds ratios (OR) for insulin resistance with increasing alcohol consumption levels across low, moderate, and high tertiles of GMS were 0.75 (95%CI 0.58-0.96), 0.82 (0.67-1), and 1.13 (0.93-1.39), respectively. We identified that individual alcohol-related species, such as Prevotella copri, Ruminococcus callidus, and Erysipelatoclostridium ramosum, modified the relationship between alcohol consumption and insulin resistance in non-carriers.

CONCLUSIONS: This study suggests that the ADH1B gene rs1229984 mutation is associated with gut microbiota profiles altered by alcohol consumption. Our findings also suggest a potential role of gut microbiota in the protective association between alcohol consumption and insulin resistance in the ADH1B variant non-carriers.}, } @article {pmid40869994, year = {2025}, author = {Peña, N and Lafuente, I and Sevillano, E and Feito, J and Allendez, G and Muñoz-Atienza, E and Crispie, F and Cintas, LM and Cotter, PD and Hernández, PE and Borrero, J}, title = {Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics.}, journal = {Genes}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/genes16080946}, pmid = {40869994}, issn = {2073-4425}, support = {2018-T1/BIO-10158//Comunidad de Madrid/ ; 2022-5A/BIO-24232//Comunidad de Madrid/ ; PEJ-2020-AI/BIO-17758//Comunidad de Madrid/ ; PID2019-104808RAI00//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Animals ; *Chickens/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Antimicrobial Peptides/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Cecum/microbiology ; }, abstract = {Background/Objectives: Antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics in livestock, offering a sustainable strategy for controlling bacterial pathogens in food production systems. In addition to their direct antimicrobial effects, AMPs play a key role in modulating host-associated microbiomes, influencing both microbial composition and function. Advances in metagenomic sequencing and bioinformatic tools now enable comprehensive exploration of AMP diversity and activity within complex microbial ecosystems. Methods: In this study, we employed Illumina-based next-generation sequencing (NGS) to analyze intestinal contents from six gut sections of broiler chickens obtained from a Spanish slaughterhouse. Results: Through de novo assembly and bioinformatic annotation, we identified biosynthetic gene clusters (BGCs) encoding ribosomally synthesized and post-translationally modified peptides (RiPPs), other specialized bioactive secondary metabolites, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and a diverse microbial community. Among all gut sections, the cecum exhibited the highest genetic richness, characterized by a high diversity of RiPP-like clusters and antimicrobial resistance determinants. Conclusions: These findings highlight the poultry gut, particularly the cecum, as a significant reservoir of antimicrobial peptides (AMPs) with potential implications in antibiotic-free poultry production and enhanced food safety.}, } @article {pmid40869080, year = {2025}, author = {Moiseenko, F and Kechin, A and Koryukov, M and Boyarskikh, U and Gabina, A and Oganesian, A and Belukhin, S and Makarkina, M and Elsakova, E and Artemeva, E and Myslik, A and Volkov, N and Bogdanov, A and Kuligina, E and Aleksakhina, S and Iyevleva, A and Ivantsov, A and Bogdanov, A and Sidorenko, S and Gostev, V and Komissarov, A and Dudurich, V and Danilov, L and Imyanitov, E and Moiseyenko, V}, title = {Interconnection of Gut Microbiome and Efficacy of Immune Checkpoint Inhibitors in Inoperable Non-Small-Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {16}, pages = {}, doi = {10.3390/ijms26167758}, pmid = {40869080}, issn = {1422-0067}, support = {125041005115-5//Russian state-funded project for ICBFM SB RAS/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Lung Neoplasms/drug therapy/microbiology/pathology ; Male ; Female ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Tumor Microenvironment/drug effects ; }, abstract = {The efficacy of immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) varies widely across patients. Growing evidence indicates that the gut microbiome, through its interaction with the tumor microenvironment, may influence the response to immunotherapy. To investigate this, we analyzed fecal and tumor samples from 63 patients with inoperable NSCLC undergoing ICI therapy. Based on microbiome profiling using 16S rRNA sequencing, patients were grouped according to treatment benefit, defined as progression-free survival (PFS) of six months or longer. Associations between α-diversity indices, microbial composition at the genus and phylum levels, and a composite Sum Index of Binary Abundance (SIBA) were examined in relation to clinical outcomes. Higher microbial α-diversity was linked to improved response to ICIs (p-value = 0.0078 for the Chao1 index). Multiple specific taxa, such as Ruminococcus gauvreauii (p-value = 2 × 10[-4]), Ruminiclostridium 9 (p-value = 8 × 10[-4]), and [Eubacterium] ventriosum (p-value = 9 × 10[-4]), were enriched in patients with favorable outcomes, whereas Oscillibacter and the Eubacterium hallii group were associated with disease progression (p-value = 2 × 10[-3] and 9 × 10[-3], respectively). The SIBA index, which reflects the absence of multiple beneficial bacterial taxa, proved to be a stronger predictor of treatment response than individual taxa alone. Median SIBA values were 18 vs. 24 in patients benefiting from IO therapy compared to non-responders (p-value = 9 × 10[-7]). These findings suggest that gut microbiome diversity and composition are closely tied to immunotherapy outcomes in NSCLC. Composite microbial metrics like SIBA may enhance predictive accuracy and inform personalized treatment approaches.}, } @article {pmid40867077, year = {2025}, author = {Ebadi, M and Reddi, S and Senyshyn, L and Minot, SS and Gooley, T and Kabage, AJ and Lee, SJ and Hill, GR and Khoruts, A and Rashidi, A}, title = {Effect of fecal microbiota transplantation on gut microbiota functional profile in recipients of allogeneic hematopoietic cell transplantation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2551882}, doi = {10.1080/19490976.2025.2551882}, pmid = {40867077}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Dysbiosis/therapy/microbiology ; Transplantation, Homologous ; Feces/microbiology ; Aged ; }, abstract = {Intestinal dysbiosis has been associated with both the effectiveness and toxicity of immunotherapy in cancer patients, inspiring multiple trials investigating fecal microbiota transplantation (FMT) in these patients. FMT restores microbial community structures damaged by antibiotics and enriches the microbiota with beneficial bacteria. However, the precise mechanism through which FMT exerts its effects and provides clinical benefits remains incompletely understood. Efforts to date have primarily focused on characterizing taxonomic changes following FMT. We hypothesized that FMT may also modify the functional pathways and metabolic capabilities of the gut microbiota, with possible clinical impact. To investigate this, we conducted a study involving 17 patients with blood disorders who received prophylactic FMT from one of the three healthy donors shortly after hematopoietic cell transplantation (HCT). By analyzing shotgun metagenomic profiles of the baseline, pre-FMT, and post-FMT gut microbiota, we demonstrate that FMT effectively restored pathways that had been depleted following HCT. However, it did not significantly reduce pathways that had expanded, indicating that FMT operates primarily through a restorative mechanism, reestablishing lost functional capabilities in the microbiota rather than suppressing overactive pathways. These findings highlight the potential for optimizing FMT protocols and identifying patient populations where FMT may be particularly beneficial.}, } @article {pmid40659786, year = {2025}, author = {Lin, NY and Fukuoka, S and Koyama, S and Motooka, D and Tourlousse, DM and Shigeno, Y and Matsumoto, Y and Yamano, H and Murotomi, K and Tamaki, H and Irie, T and Sugiyama, E and Kumagai, S and Itahashi, K and Tanegashima, T and Fujimaki, K and Ito, S and Shindo, M and Tsuji, T and Wake, H and Watanabe, K and Maeda, Y and Enokida, T and Tahara, M and Yamashita, R and Fujisawa, T and Nomura, M and Kawazoe, A and Goto, K and Doi, T and Shitara, K and Mano, H and Sekiguchi, Y and Nakamura, S and Benno, Y and Nishikawa, H}, title = {Microbiota-driven antitumour immunity mediated by dendritic cell migration.}, journal = {Nature}, volume = {644}, number = {8078}, pages = {1058-1068}, pmid = {40659786}, issn = {1476-4687}, mesh = {Animals ; *Dendritic Cells/immunology/cytology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Cell Movement/immunology ; Humans ; Female ; CD8-Positive T-Lymphocytes/immunology/cytology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology/metabolism ; Tumor Microenvironment/immunology ; Integrin alpha Chains/metabolism ; Male ; *Neoplasms/immunology/microbiology/therapy/pathology/drug therapy ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Antigens, CD/metabolism ; Feces/microbiology ; Cell Line, Tumor ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; }, abstract = {Gut microbiota influence the antitumour efficacy of immune checkpoint blockade[1-6], but the mechanisms of action have not been fully elucidated. Here, we show that a new strain of the bacterial genus Hominenteromicrobium (designated YB328) isolated from the faeces of patients who responded to programmed cell death 1 (PD-1) blockade augmented antitumour responses in mice. YB328 activated tumour-specific CD8[+] T cells through the stimulation of CD103[+]CD11b[-] conventional dendritic cells (cDCs), which, following exposure in the gut, migrated to the tumour microenvironment. Mice showed improved antitumour efficacy of PD-1 blockade when treated with faecal transplants from non-responder patients supplemented with YB238. This result suggests that YB328 could function in a dominant manner. YB328-activated CD103[+]CD11b[-] cDCs showed prolonged engagement with tumour-specific CD8[+] T cells and promoted PD-1 expression in these cells. Moreover, YB238-augmented antitumour efficacy of PD-1 blockade treatment was observed in multiple mouse models of cancer. Patients with elevated YB328 abundance had increased infiltration of CD103[+]CD11b[-] cDCs in tumours and had a favourable response to PD-1 blockade therapy in various cancer types. We propose that gut microbiota enhance antitumour immunity by accelerating the maturation and migration of CD103[+]CD11b[-] cDCs to increase the number of CD8[+] T cells that respond to diverse tumour antigens.}, } @article {pmid40129370, year = {2025}, author = {Lázaro, Á and Gómez-Ramírez, P and Vila-Donat, P and Cimbalo, A and Manyes, L}, title = {Effects of pumpkin and fermented whey on fecal microbiota profile against AFB1 and OTA exposure in Wistar rats.}, journal = {Toxicology mechanisms and methods}, volume = {35}, number = {7}, pages = {716-728}, doi = {10.1080/15376516.2025.2484636}, pmid = {40129370}, issn = {1537-6524}, mesh = {Animals ; Rats, Wistar ; Male ; Female ; *Feces/microbiology ; *Ochratoxins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Aflatoxin B1/toxicity ; *Cucurbita ; Rats ; Fermentation ; Bacteria/drug effects/genetics ; }, abstract = {Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28-day exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA, and AFB1+OTA), while there was an increase-although not in all groups-when adding the functional ingredients. The main difference between the sexes was found in FW+AFB1+OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.}, } @article {pmid40863630, year = {2025}, author = {Hu, GA and Sun, HY and Yin, QJ and Wang, H and Liu, SY and Wang, BG and Wang, H and Li, X and Wei, B}, title = {Exploring the Biosynthetic Potential of Microorganisms from the South China Sea Cold Seep Using Culture-Dependent and Culture-Independent Approaches.}, journal = {Marine drugs}, volume = {23}, number = {8}, pages = {}, pmid = {40863630}, issn = {1660-3397}, support = {2022YFC2804700//National Key Research and Development Program/ ; 42276137//National Natural Science Foundation of China/ ; RF-A2022013//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; }, mesh = {China ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Secondary Metabolism/genetics ; *Microbiota/genetics ; *Bacteria/genetics/metabolism ; *Seawater/microbiology ; Ecosystem ; Oceans and Seas ; }, abstract = {Cold seep ecosystems harbor unique microbial communities with potential for producing secondary metabolites. However, the metabolic potential of cold seep microorganisms in the South China Sea remains under-recognized. This study employed both culture-dependent and culture-independent approaches, including 16S rRNA amplicon sequencing and metagenomics, to investigate microbial communities and their potential for secondary metabolite production in the South China Sea cold seep. The results indicate microbial composition varied little between two non-reductive sediments but differed significantly from the reductive sediment, primarily due to Planctomycetes and Actinobacteria. Predicting the Secondary Metabolism Potential using Amplicon (PSMPA) predictions revealed 115 strains encoding more than 10 biosynthetic gene clusters (BGCs), with lower BGC abundance in reductive sediment. Culture-dependent studies showed Firmicutes as the dominant cultivable phylum, with strains from shallow samples encoding fewer BGCs. Metagenomic data confirmed distinct microbial compositions and BGC distributions across sediment types, with cold seep type having a stronger influence than geographic location. Certain BGCs showed strong correlations with sediment depth, reflecting microbial adaptation to nutrient-limited environments. This study provides a comprehensive analysis of the metabolic capabilities of South China Sea cold seep microorganisms and reveals key factors influencing their secondary metabolic potential, offering valuable insights for the efficient exploration of cold seep biological resources.}, } @article {pmid40863548, year = {2025}, author = {García-Muñoz, A and Pino-Bodas, R}, title = {Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data: Solorina crocea (Peltigerales, Ascomycota) as a Case Study.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {40863548}, issn = {2309-608X}, support = {CNS2022-135904//Agencia Estatal de Investigación/ ; 2020-T1/AMB-19852//CAM Atracción de Talento program/ ; }, abstract = {The advent of next-generation sequencing technologies has given rise to considerably diverse techniques. However, integrating data from these technologies to generate high-quality genomes remains challenging, particularly when starting from metagenomic data. To provide further insight into this process, the genome of the lichenized fungus Solorina crocea was sequenced using DNA extracted from the thallus, which contains the genome of the mycobiont, along with those of the photobionts (a green alga and a cyanobacterium), and other associated microorganisms. Three different strategies were assessed for the assembly of a de novo genome, employing data obtained from Illumina and PacBio HiFi technologies: (1) hybrid assembly based on metagenomic data; (2) assembly based on metagenomic long reads and scaffolded with filtered mycobiont long and short reads; (3) hybrid assembly based on filtered mycobiont short and long reads. Assemblies were compared according to contiguity and completeness criteria. Strategy 2 achieved the most continuous and complete genome, with a size of 55.5 Mb, an N50 of 148.5 kb, and 519 scaffolds. Genome annotation and functional prediction were performed, including identification of secondary metabolite biosynthetic gene clusters. Genome annotation predicted 6151 genes, revealing a high number of genes associated with transport, carbohydrate metabolism, and stress response.}, } @article {pmid40863514, year = {2025}, author = {Alcaíno, J and Veloso, C and Coche, M and Troncoso, D and Baeza, M}, title = {Fungi in the Chilean Altiplano: Analyses of Diversity and Yeasts with Applied Enzymatic Potential.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {40863514}, issn = {2309-608X}, support = {Fondecyt 1230427//Agencia Nacional de Investigacion y Desarrollo de Chile/ ; }, abstract = {Fungal communities in high plateau ecosystems remain understudied despite their crucial roles in soil ecosystems, and yeasts inhabiting extreme regions have potential for industrial and biotechnological applications. We studied the fungal diversity in soils across 14 Chilean Altiplano sites using amplicon-based metagenomics and isolation of yeasts to assess their growth under various conditions and hydrolytic enzyme secretion. Using the metagenomic approach, the Ascomycota and Basidiomycota phyla were found to be the most abundant (85% and 8%, respectively). Unclassified families and genera prevailed at six and ten sites, respectively. At the other sites, the most abundant families included Cladosporiaceae, Teratosphaeriaceae, and Sporormiaceae, and the genera Oleoguttula, Coniochaeta, and Peziza. Biodiversity indices did not correlate with the soil's geographic origin, organic matter content, humidity, or pH. Most isolated yeasts belong to the Naganishia, Holtermanniella, and Vishniacozyma genera, growing at temperatures ranging from 4 °C to 26 °C. Most isolates could use glucose, sucrose, and maltose as carbon sources and exhibited amylase, esterase, pectinase, and protease activities at 30 °C and below. Our results indicate that the evaluated soil physicochemical parameters do not explain the fungal distribution in the Altiplano and highlight the region as a reservoir of unknown fungi, including yeasts with industrially relevant enzymes.}, } @article {pmid40862113, year = {2025}, author = {Wang, W and Wang, L and Chen, J and Yang, X and Guo, Q and Zhang, Z and Liang, J and Gu, P and Shao, J}, title = {The gut microbiome: a vital link to hyperuricemia, gout and acute flares?.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1643566}, pmid = {40862113}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Hyperuricemia/microbiology ; *Gout/microbiology ; Male ; Middle Aged ; Female ; Adult ; Uric Acid/blood ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; Feces/microbiology ; Bacteria/genetics/classification ; }, abstract = {OBJECTIVES: To explore the associations between the gut microbiome and asymptomatic hyperuricemia, as well as acute gout flares.

METHODS: Forty-three Chinese participants were divided into healthy and hyperuricemic groups according to serum uric acid (SUA) levels. The hyperuricemia group were further separated into asymptomatic hyperuricemia (HUA) and gout patients on the basis of their clinical symptoms. In addition, the gout group was further divided into intercritical gout and acute gout groups on the basis of the claim of joint pain and relevant clinical parameters. 16S rRNA sequencing was used to evaluate the microbiome composition of all the groups.

RESULTS: A dramatic decreasing trend in microbial richness and diversity was observed in hyperuricemic patients compared with healthy controls. The same decreasing trend in microbial relative abundance was also observed. The butyrate-producing genera Faecalibacterium, Coprococcus and Enterococcus were markedly decreased in hyperuricemic patients. Moreover, opportunistic pathogens, such as the phylum Proteobacteria and genus Fusobacterium, were enriched in the hyperuricemia group. Furthermore, the gut microbiota of gout patients also exhibited significantly reduced microbial diversity compared with asymptomatic hyperuricemic patients, characterized by decreased richness of the genera Dialister, Ruminococcus, and Faecalibacterium. Greater differences in microbial richness and diversity can still be observed when gout flares occur. The abundances of Bacteroides and Lachnospira genera decreased in the acute gout stage.

CONCLUSION: Our study revealed that community richness and diversity change during the process of gout or HUA, especially during acute gout flares. Metagenomic species were significantly altered during different stages of hyperuricemia.}, } @article {pmid40859872, year = {2025}, author = {Bunka, L and Rozenberga, M and Silamiķelis, I and Saksis, R and Birzniece, L and Megnis, K and Fedulovs, A and Pahirko, L and Zaļizko, P and Krustiņš, E and Kloviņš, J and Sokolovska, J and Elbere, I}, title = {Dual-approach analysis of gut microbiome in patients with type 1 diabetes and diabetic kidney disease.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2531254}, pmid = {40859872}, issn = {1365-2060}, mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology/complications ; *Diabetic Nephropathies/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Middle Aged ; Disease Progression ; Metagenomics/methods ; Biopsy ; Young Adult ; Bacteroides/isolation & purification/genetics ; }, abstract = {BACKGROUND: Type 1 diabetes (T1D) is a multifactorial autoimmune disease mediated by genetic, epigenetic, and environmental factors. Diabetic kidney disease (DKD) is a major complication of diabetes mellitus which affects 30-40% of T1D patients. Increasing evidence suggests the significant role of the microbiome in the progression of both T1D and DKD.

MATERIALS AND METHODS: Here we recruited 76 T1D patients and 22 healthy controls and combined data from sigmoid colon biopsy samples analysed with V3-V4 region amplification of 16S rRNA gene and shotgun metagenomics data obtained from faecal samples. Additionally, we compared T1D patients with and without progression of DKD.

RESULTS: We observed significant differences within both sample types at various taxonomic and functional levels. T1D patient microbiota detected using biopsy samples had a lower abundance of the Bacteroides genus when compared to healthy controls. Significantly, despite only a few taxonomic differences patients with and without DKD progression were vastly different at the functional pathway level within the faecal samples - we observed 2 and 61 enriched pathways in these groups. respectively, with several of these pathways linked to the mediation of renal function.

CONCLUSION: Altogether, we present novel data about microbial signatures relevant to T1D and DKD progression, which partly supports previous data and also presents possible tissue type or population-specific elements. DKD progression is characterized with significant differences within the functional level of the gut microbiome.}, } @article {pmid40859318, year = {2025}, author = {Lin, Z and Jiang, Y and Liu, H and Yang, J and Yang, B and Zhang, K and Tang, P and Xiang, B and Sun, B}, title = {Airway microbiota and immunity associated with chronic obstructive pulmonary disease severity.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {962}, pmid = {40859318}, issn = {1479-5876}, support = {GMUCR2024-02009//Major clinical research project of Guangzhou Medical University/ ; 2023B110008//Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases/ ; }, mesh = {*Pulmonary Disease, Chronic Obstructive/immunology/microbiology/pathology/genetics ; Humans ; *Microbiota ; *Severity of Illness Index ; Male ; Female ; Aged ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Immunity ; Cohort Studies ; Biomarkers/metabolism ; Dysbiosis ; Reproducibility of Results ; *Respiratory System/microbiology ; Metagenomics ; Bacteria ; }, abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is characterized by progressive airflow limitation and chronic inflammation. Although airway microbes and host immunity are known contributors, the molecular mechanisms underlying disease severity remain unclear. This study explores microbial dysbiosis and host immune responses across varying COPD severities.

METHODS: We conducted integrated metagenomic and transcriptomic analyses on bronchoalveolar lavage fluid from two cohorts: a discovery cohort and a validation cohort. We investigated microbial diversity, pathogenic bacterial enrichment, and host gene expression patterns. Functional metagenomics was used to assess antibiotic resistance genes. Host-microbe network analyses explored correlations between pathogens and immune-metabolic pathways. Diagnostic models utilizing microbial-immune biomarkers were developed, trained on a subset of the discovery cohort, tested on remaining discovery samples, and validated by quantitative polymerase chain reaction (qPCR) in the validation cohort to distinguish COPD from controls and stratify disease severity.

RESULTS: Severe COPD exhibited reduced microbial diversity and an increased presence of pathogenic bacteria, including Moraxella osloensis and Streptococcus species. These pathogens were associated with dysregulated inflammatory signaling, and significant neutrophil activity, evidenced by the formation of Neutrophil Extracellular Traps (NETs), and oxidative stress, which correlated with airway remodeling and a decline in lung function. Functional metagenomics showed a significant increase in antibiotic resistance genes in severe cases, linked to chronic treatment pressures. Host-microbe network analyses revealed strong correlations between these pathogens and disrupted immune-metabolic pathways, such as altered energy metabolism and inflammatory cascades, consistent across both cohorts. Diagnostic models based on microbial-immune biomarkers demonstrated high accuracy in differentiating COPD patients from controls and in stratifying disease severity.

CONCLUSIONS: This study identifies microbial and immune signatures associated with COPD severity, providing mechanistic insights into its pathophysiology. The findings may inform precision medicine strategies by targeting airway dysbiosis and immune dysregulation. While causal relationships could not be established in this cross-sectional study, the findings provide a foundation for future mechanistic investigations using advanced in vitro and in vivo models.}, } @article {pmid40858544, year = {2025}, author = {Zou, X and Cao, H and Hong, L and Suo, L and Wang, C and Chang, K and Ni, Y and Liu, B and Cao, B}, title = {Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.}, journal = {Signal transduction and targeted therapy}, volume = {10}, number = {1}, pages = {272}, pmid = {40858544}, issn = {2059-3635}, mesh = {Humans ; *Immunity, Innate/genetics/immunology ; Mice ; Animals ; *Influenza, Human/immunology/microbiology/genetics ; Female ; Male ; *Streptococcus oralis/immunology/pathogenicity/genetics ; Middle Aged ; *Microbiota/immunology/genetics ; Gastrointestinal Microbiome/immunology/genetics ; Aged ; Probiotics ; }, abstract = {Respiratory microbial dysbiosis has been implicated in the occurrence and progression of community-acquired pneumonia (CAP). However, the dynamic variation in the respiratory microbiota and its interaction with the host response remain poorly understood. Here, we performed metagenomic analysis of respiratory and gut microbiota, along with blood transcriptomics, using longitudinally collected samples from 38 CAP patients. CAP patients presented disrupted sputum microbiota at the early, middle, and late stages of hospitalization. Microbial pathways involved in peptidoglycan biosynthesis and immune evasion, particularly contributed by the Streptococcus genus, were enriched in CAP patients. Additionally, several Streptococcus strains demonstrated correlation between respiratory and gut microbiota in CAP patients. By incorporating host response data, we revealed that Streptococcus oralis (SOR) was associated with host pathways involved in the innate immune response to infection, and this microbe‒host interaction was reproduced in a newly enrolled CAP cohort consisting of 22 patients with influenza infection. The host-SOR interaction was validated in a mouse model, where SOR demonstrated protective efficacy against influenza virus infection comparable to that of the well-established respiratory probiotic Lactobacillus rhamnosus GG. Preaspiration of SOR in mice significantly mitigated body weight loss, reduced lung inflammation, and lowered viral loads following influenza virus challenge. Host response profiling indicated that SOR priming activated a greater innate immune response at the early stage of infection and that this response resolved timely as the host began to recover. These findings suggest that respiratory commensals play an immune-protective role by inducing a timely innate immune response to prevent CAP progression.}, } @article {pmid40856764, year = {2025}, author = {Sharma, P and Iqbal, MZ and Chandra, R}, title = {Bacterial allies in chromium hyperaccumulation: native rhizobacterial dynamics of profusely growing Dactyloctenium aegyptium in highly tainted tannery sludge.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {9}, pages = {314}, pmid = {40856764}, issn = {1573-0972}, support = {IF210284//Department of Science and Technology, Ministry of Science and Technology, India/ ; }, mesh = {*Chromium/metabolism ; Biodegradation, Environmental ; *Sewage/microbiology/chemistry ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Plant Roots/microbiology/metabolism ; Soil Pollutants/metabolism ; Tanning ; Soil Microbiology ; Microbiota ; Rhizosphere ; Industrial Waste ; }, abstract = {Tannery sludge has highly toxic heavy metals like chromium (Cr), posing environmental and health risks. This research investigates the potential of Dactyloctenium aegyptium (L.) Willd. and the associated rhizobacterial communities for bacterial-assisted phytoremediation of tannery sludge, having 6403.16 ± 0.71 mg/kg Cr. The analyses of culturable bacterial communities resulted in the exploration of two highly potent plant growth-promoting strains (CRB2 and CRB5), out of the six culturable strains obtained. SEM imaging depicted robust bacterial colonization on the plant root surface, confirming active plant-microbe interaction. D. aegyptium showed significant Cr accumulation (4936 ± 1.34 mg/kg) within the tissues, followed by substantial translocation to shoots and leaves (TF = 1.01). With a BCF of 1.66 for Cr, D. aegyptium bespeaks evident hyperaccumulation potential. TEM imaging revealed the granular metal deposition in the plant tissues. Post-plant growth, the sludge exhibited an 80.3% reduction in Cr concentration, alongside enhanced physicochemical properties (reduced pH, increased organic matter, reduced metal content). Furthermore, metagenomics analyses showed that the growth of D. aegyptium drastically changed rhizobacterial communities, decreasing species richness and increasing functional pathways associated with stress responses and metal tolerance. Important genes (copA, czcA, nirA), enzymes (dioxygenases, trimethylamine-N-oxide reductase), and proteins (CsgE, DsbG), essential for the nitrogen cycle, chromium detoxification, and plant-microbe associations, were found to be involved in metabolic pathways. The study amalgamates morphophysiological and advanced metagenomic approaches to put forth an understanding of species-specific plant-microbe interactions for the development of scalable and sustainable remediation and engineering of rhizospheric microbiomes for eco-restoration of heavy metal-polluted industrial sites.}, } @article {pmid40855532, year = {2025}, author = {Babalola, OO and Ogundeji, FO and Akanmu, AO}, title = {Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {60}, pmid = {40855532}, issn = {2730-6844}, support = {UID123634 and UID132595//National Research Foundation/ ; }, mesh = {*Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/genetics/classification ; Fungi/genetics/classification ; *Apium/microbiology ; Metagenomics ; Microbiota ; Phylogeny ; }, abstract = {OBJECTIVES: This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.

DATA DESCRIPTION: The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).}, } @article {pmid40855409, year = {2025}, author = {Graeber, E and Tysha, A and Nisar, A and Wind, D and Mendling, W and Finzer, P and Dilthey, A}, title = {Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {544}, pmid = {40855409}, issn = {1471-2180}, mesh = {Female ; Humans ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Vaginosis, Bacterial/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Adult ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; Young Adult ; DNA, Bacterial/genetics ; Cohort Studies ; Nanopores ; }, abstract = {BACKGROUND: The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, 16S rRNA gene sequencing-based approaches have been used to characterize the composition of vaginal microbiomes, but shallow shotgun metagenomic sequencing (SMS) approaches, in particular when implemented with the Oxford Nanopore Technologies, have important potential advantages with respect to cost effectiveness, speed of data generation, and the availability of flexible multiplexing schemes.

RESULTS: Based on a study cohort of n = 52 women, of which 23 were diagnosed with BV, we evaluated the applicability of Nanopore-based SMS for the characterization of vaginal microbiomes in direct comparison to Illumina 16S-based sequencing. We observed perfect agreement between the two approaches with respect to detecting the dominance of individual samples by either Lactobacilli, vaginosis-associated, or other taxa; very high concordance (92%) with respect to community state type (CST) classification; and a high degree of concordance with respect to the overall clustering structures of the sequenced microbiomes. Comparing the inferred abundances of individual species in individual samples, we observed significant differences (Wilcoxon signed-rank test p < 0.05) between the two approaches for 12 of the 20 species most abundant in our cohort, indicating differences in the fine-scale characterization of vaginal microbiomes. Higher overall abundance of Gardnerella vaginalis, associated with an increased number of CST IV detections, in the Nanopore shallow SMS data indicated potentially increased sensitivity of this approach to dysbiotic states of the vaginal microbiome. Nanopore shallow SMS also enabled the methylation-based quantification of different human cell types in the characterized samples as well as the detection of non-prokaryotic species, including Lactobacillus phage and Candida albicans in study participants with microscopically detected Candida. One important potential limitation of the evaluated Nanopore-based SMS approach was marked variation in sequencing yields.

CONCLUSION: Our study demonstrated the successful application and potential advantages of Nanopore-based shallow SMS for the characterization of vaginal microbiomes and paves the way for its application in larger-scale research or diagnostic settings.}, } @article {pmid40854874, year = {2025}, author = {Kaelin, EA and Mitchell, C and Soria, J and La Rosa, A and Ticona, E and Coombs, RW and Frenkel, LM and Bull, ME and Lim, ES}, title = {Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7904}, pmid = {40854874}, issn = {2041-1723}, support = {R00DK107923//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Female ; Humans ; Peru ; *HIV Infections/drug therapy/virology/microbiology ; *Virome/genetics ; *Virus Shedding/drug effects ; Adult ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Microbiota/genetics ; Longitudinal Studies ; HIV-1/physiology ; Middle Aged ; CD4 Lymphocyte Count ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Viral Load ; Anti-HIV Agents/therapeutic use ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Despite successful suppression of plasma HIV replication by antiretroviral therapy (ART), some women living with HIV (WLHIV) can still experience genital HIV shedding (discordant shedding). Female genital tract (FGT) bacterial and viral microbiome (bacteriome and virome) community dynamics during long-term ART in WLHIV are poorly understood but might contribute to discordant HIV shedding, as the bacteriome and virome are known to influence FGT health. Here, using metagenomic next-generation sequencing, we characterize the bacteriome and virome in 125 cervicovaginal specimens collected over two years from 31 WLHIV in Lima, Peru, and show that FGT bacteriome instability is associated with discordant HIV shedding, while longitudinal changes in FGT virome composition are associated with ART duration. Intrapersonal bacteriome variation is higher in discordant HIV shedders compared to non-shedders. Cervicovaginal virome composition changes over time, particularly in non-shedders. Specifically, anellovirus relative abundance is inversely associated with ART duration and CD4 counts. Our results suggest that discordant HIV shedding is linked with FGT bacteriome instability, and immune recovery during ART influences FGT virome composition.}, } @article {pmid40828281, year = {2025}, author = {Enciso Garcia, JS and Chignola, M and Ragionieri, L and Rey, F and Fluch, M and Borruso, L and Corretto, E and Schuler, H}, title = {High-Throughput Amplicon Sequencing for Analyzing Microbial Communities of Insects.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2935}, number = {}, pages = {237-258}, pmid = {40828281}, issn = {1940-6029}, mesh = {Animals ; *Insecta/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Insects represent more than 80% of all described species on the planet. This diversity is a result of millions of years of evolution, during which insects have colonized nearly every habitat. Their success is partly due to their ability to form symbiotic relationships with a wide variety of other organisms, especially microorganisms. Identifying and characterizing associated microorganisms are crucial to understanding the complexity and dynamics of these symbiotic relationships. To date, advancements in sequencing technologies that provide large sequence data sets have become ideal tools for characterizing insect microbiomes, including information about non-cultivable microorganisms commonly found in insects. Despite the growing number of studies focused on insect microbiome characterization, there are few protocols detailing methodological procedures for fieldwork, DNA extraction, and data processing. Here, we present an overview of the characterization of insect-associated bacterial communities. We cover best practices for data interpretation and visualization, including alpha and beta diversity analyses, community composition profiling, and statistical testing to identify microbial associations of insects.}, } @article {pmid40822586, year = {2025}, author = {Dharmalingam, D and Semalaiyappan, J and Thirumal, S and Kuttiatt, VS}, title = {Unveiling Facklamia: detection of an emerging microbe in the skin microbiome of patients with filarial lymphedema.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1624288}, pmid = {40822586}, issn = {2235-2988}, mesh = {Humans ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Lymphedema/microbiology ; Male ; *Elephantiasis, Filarial/microbiology ; Female ; Middle Aged ; DNA, Ribosomal/genetics/chemistry ; Adult ; DNA, Bacterial/genetics/chemistry ; Metagenomics ; Sequence Analysis, DNA ; Skin Microbiome ; }, abstract = {Facklamia is an emerging pathogen in human beings and only a few clinical cases were reported in the literature. We detected the presence of this unusual microbe among the skin flora of three patients with filarial lymphedema in a 16S rRNA-based metagenomic study on the skin microbiome. To our knowledge, this is the first report of detection of this microbe in patients affected with filarial lymphedema. Further investigations are required to elucidate the role of Facklamia in secondary skin and soft tissue infection of filarial lymphedema patients.}, } @article {pmid40822578, year = {2025}, author = {Wu, X and Zhu, H and Hu, Y and Zhang, L and Huang, L}, title = {Meta-analysis of H. pylori and the gut microbiome interactions and clinical outcomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1610523}, pmid = {40822578}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Helicobacter pylori/genetics ; *Helicobacter Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Gastritis/microbiology ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Stomach Neoplasms/microbiology ; }, abstract = {INTRODUCTION: Helicobacter pylori is a globally prevalent gastric pathogen associated with chronic gastritis, peptic ulcers, and gastric cancer. Its interaction with the gut microbiome (GM), a dynamic microbial community within the gastrointestinal tract, plays a critical role in modulating host immune responses and disease progression. This study aimed to investigate the complex interactions between H. pylori infection and the GM and to evaluate how microbiome alterations relate to clinical outcomes such as gastritis, ulcers, and gastric cancer.

METHODS: A meta-analysis was conducted using publicly available 16S rRNA and shotgun metagenomic datasets. Microbiome composition differences were assessed using differential abundance analysis, alpha- and beta-diversity metrics, and principal component analysis (PCA). Random forest models were employed to predict the clinical outcomes based on microbiome and clinical data. Hyperparameter tuning and cross-validation were applied to ensure model robustness.

RESULTS: The analysis revealed significant microbial shifts associated with H. pylori infection, including enrichment of Proteobacteria, Fusobacterium spp., and Prevotella spp., and depletion of beneficial taxa like Lactobacillus spp. and Faecalibacterium prausnitzii. Microbial diversity declined progressively with disease severity. Predictive models demonstrated high accuracy (89.3%) in classifying the disease states and identifying key microbial biomarkers such as Fusobacterium spp. and Bacteroides fragilis with strong predictive power.

DISCUSSION: This study highlights the critical role of GM dysbiosis in H. pylori-related disease progression. The identified microbial signatures and predictive models offer promising tools for early diagnosis, risk stratification, and personalized treatment of H. pylori-associated gastrointestinal disorders. Future integration of multi-omics data may further unravel the microbial mechanisms and support microbiome-based precision medicine.}, } @article {pmid40819131, year = {2025}, author = {Tang, B and Li, S and Li, X and He, J and Zhou, A and Wu, L and Xiao, X and Wang, S and Jiang, H and Jian, J and Hou, Z and Ge, Y and Lei, Y and Zhou, J and Tu, D and Lu, C and Yang, M and Yang, S}, title = {Cholecystectomy-related gut microbiota dysbiosis exacerbates colorectal tumorigenesis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7638}, pmid = {40819131}, issn = {2041-1723}, support = {82030020//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172958//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology/genetics ; *Colorectal Neoplasms/microbiology/etiology/pathology/metabolism ; *Dysbiosis/microbiology/etiology ; Humans ; Mice ; *Carcinogenesis/pathology/metabolism/drug effects ; *Cholecystectomy/adverse effects ; Receptors, Cytoplasmic and Nuclear/metabolism/agonists ; Chenodeoxycholic Acid/analogs & derivatives/pharmacology ; Bile Acids and Salts/metabolism ; Male ; Mice, Inbred C57BL ; Taurochenodeoxycholic Acid/metabolism ; Female ; Fecal Microbiota Transplantation ; beta Catenin/metabolism ; Disease Models, Animal ; Ruminococcus ; }, abstract = {Cholecystectomy represents the most prevalent biliary surgical procedure for gallbladder abnormalities. Growing evidence suggests that cholecystectomy is associated with an elevated risk of colorectal cancer. However, the underlying mechanism remains elusive. Here we show that cholecystectomy exacerbates colorectal tumorigenesis in both AOM/DSS and APC[min/+] mice models. Metagenomic sequencing and targeted metabolomics show that cholecystectomy leads to a decrease of Bifidobacterium breve (B. breve) and an increase of Ruminococcus gnavus (R. gnavus), along with increased levels of glycoursodeoxycholic acid (GUDCA) in human and tauroursodeoxycholic acid (TUDCA) in mice. Fecal microbiota transplantation, single bacterial colonization and bile acid supplementation demonstrate that cholecystectomy-related gut microbiota perturbations promote the production of TUDCA and facilitate colorectal tumorigenesis. RNA-sequencing and co-immunoprecipitation reveal that the compromised bile acid metabolism inhibits farnesoid X receptor (FXR) signaling, disrupts the FXR/β-catenin interaction, and ultimately exacerbates colorectal tumorigenesis. Significantly, FXR agonist obeticholic acid (OCA) averts cholecystectomy-related colorectal tumorigenesis. The gut microbiota holds a crucial position in cholecystectomy-induced colorectal tumorigenesis, and modulation of the gut microbiota-bile acid-FXR axis represents a promising preventive strategy.}, } @article {pmid40813371, year = {2025}, author = {Kiu, R and Darby, EM and Alcon-Giner, C and Acuna-Gonzalez, A and Camargo, A and Lamberte, LE and Phillips, S and Sim, K and Shaw, AG and Clarke, P and van Schaik, W and Kroll, JS and Hall, LJ}, title = {Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7569}, pmid = {40813371}, issn = {2041-1723}, support = {100974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S017941/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Probiotics/administration & dosage/pharmacology ; *Infant, Very Low Birth Weight ; *Anti-Bacterial Agents/pharmacology/therapeutic use/adverse effects ; Infant, Newborn ; Infant, Premature ; Feces/microbiology ; Female ; Male ; Gene Transfer, Horizontal ; Metagenomics ; Milk, Human ; Enterococcus/genetics/drug effects ; Metagenome ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.g., certain Bifidobacterium strains) may help restore a healthy gut microbiota. In this study, we investigated the effects of probiotics and antibiotics on the gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants - one of which received probiotics. Within each group, some infants received antibiotics (benzylpenicillin and/or gentamicin), while others did not. Using shotgun metagenomic sequencing on 92 longitudinal faecal samples, we reconstructed >300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.}, } @article {pmid40813370, year = {2025}, author = {Rakoff-Nahoum, S and Debelius, J and Valles-Colomer, M and Noordzij, HT and Esteban-Torres, M and Zhernakova, A and Brusselaers, N and Pettersen, VK}, title = {A reconceptualized framework for human microbiome transmission in early life.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7546}, pmid = {40813370}, issn = {2041-1723}, mesh = {Humans ; *Microbiota/physiology/genetics ; Metagenomics/methods ; }, abstract = {Human development and physiology are fundamentally linked with the microbiome. This is particularly true during early life, a critical period for microbiome assembly and its impact on the host. Understanding microbial acquisition in early life is thus central to both our basic understanding of the human microbiome and strategies for disease prevention and treatment. Here, we review the historical approaches to categorize microbial transmission originating from the fields of infectious disease epidemiology and evolutionary biology and discuss how this lexicon has influenced our approach to studying the early-life microbiome, often leading to confusion and misinterpretation. We then present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when. We present ways these parameters may be assigned, with a particular focus on the 'transmitted strain' through metagenomics to capture these elements. We end with a discussion of approaches for implementing this framework toward defining each component of microbiome acquisition.}, } @article {pmid40813051, year = {2025}, author = {An, FJ and Niu, ZR and Liu, TN and Su, YZ}, title = {[Structure and Metabolic Function Characteristics of Soil Bacterial Communities under Different Vegetation Types in Arid Region].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {8}, pages = {5360-5368}, doi = {10.13227/j.hjkx.202407230}, pmid = {40813051}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Desert Climate ; China ; *Bacteria/metabolism/classification ; *Ecosystem ; Soil/chemistry ; Biodiversity ; Plants/classification ; Plant Development ; }, abstract = {The aim of this study was to explore the effects of different vegetation types on soil bacterial community structure and metabolic function in an oasis-desert ecotone and provide scientific theoretical basis for species allocation and management of vegetation reconstruction in arid desert ecosystem. Nitraria sphaerocarpa Maxim and Calligonum mongolicum Turcz are the main natural vegetation, Haloxylon ammodendron Bunge, and Hedysarum scoparium Fisch are the primary artificial vegetation, and Ha-Cm are the main mixed community in an oasis-desert ecotone in northwest China. Understanding soil microbial community structure and function under typical vegetation types is crucial for accurate management and sustainable use of desert vegetation. We used high-throughput sequencing technology to explore the effects of different vegetation types on the structure, diversity, and metabolic pathways of soil bacteria and to investigate the key factors driving the change of soil bacterial community structure. The results showed that the growth of artificial vegetation and natural vegetation significantly increased the richness and diversity of the soil bacterial community, but no significant difference was observed. Metagenomic analysis showed that the same dominant bacterial phyla existed in all soils, but the proportions were different. Actinobacteriota, Proteobacteria, and Chloroflexi were the absolute dominant bacterial phyla, accounting for 65.12%-78.68% of the total bacteria. Principal co-ordinates analysis showed significant differences in soil bacterial community structure in the planted forest but similarities in the natural forest. The metabolic pathways of soil bacteria in different vegetation communities were similar. Soil organic carbon （SOC）, available phosphorus （AP）, and pH were important abiotic factors affecting the functional structure of bacteria. The findings are helpful for furthering the understanding of plant-soil interaction in ecologically fragile deserts.}, } @article {pmid40812187, year = {2025}, author = {Tričković, M and Kieser, S and Zdobnov, EM and Trajkovski, M}, title = {Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.}, journal = {Cell host & microbe}, volume = {33}, number = {8}, pages = {1446-1458.e4}, doi = {10.1016/j.chom.2025.07.015}, pmid = {40812187}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Colorectal Neoplasms/microbiology/diagnosis ; *Bacteria/classification/genetics/isolation & purification ; Machine Learning ; Species Specificity ; }, abstract = {Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associations and hinder deductive research. Here, we comprehensively define the human gut microbiota at a consistently annotated operational subspecies unit (OSU) resolution in an unbiased, cohort-independent manner, demonstrating that this approach can generalize across diverse global populations while maintaining specificity and improving interstudy reproducibility. We develop panhashome-a sketching-based method for rapid subspecies and species quantification and identification of genes that drive intraspecies variations-and show that subspecies carry implicit information undetectable at the species level. We identify subspecies associated with colorectal cancer (CRC) whose sibling subspecies or species are not, while a machine-learning CRC diagnostic algorithm based on subspecies outperformed species-level methods. This subspecies catalog allows identification of genes that drive functional differences between subspecies as a fundamental step in mechanistically understanding microbiome-phenotype interactions.}, } @article {pmid40810759, year = {2025}, author = {Frere Martiniuc, C and de Assis Leite, DC and Seldin, L and Jurelevicius, D}, title = {Viral Diversity in Polar Hydrocarbon-Contaminated Soils: A Transect Study from King George Island, Antarctica.}, journal = {Food and environmental virology}, volume = {17}, number = {3}, pages = {43}, pmid = {40810759}, issn = {1867-0342}, mesh = {Antarctic Regions ; *Soil Microbiology ; *Viruses/classification/genetics/isolation & purification ; *Soil Pollutants/analysis/metabolism ; *Hydrocarbons/analysis/metabolism ; Polycyclic Aromatic Hydrocarbons/analysis/metabolism ; Soil/chemistry ; Metagenomics ; Biodiversity ; Bacteria/classification/genetics/isolation & purification/metabolism ; Phylogeny ; Metagenome ; }, abstract = {Viruses are key components of soils, influencing microbial dynamics and biogeochemical cycles. Here, we used shotgun metagenomics to analyze the virome of hydrocarbon-contaminated and uncontaminated soils from King George Island, Antarctica. Viral sequences were obtained from metagenomes of all soils; however, the relative abundance of viruses was higher in hydrocarbon-contaminated soils compared to uncontaminated soils. Our results indicate that viral distribution correlates with polycyclic aromatic hydrocarbons (PAHs) in King George Island soil (p = 0.05). Taxonomic analysis of viral contigs revealed viruses from realms Duplodnaviria, Varidnaviria, Monodnaviria, and Riboviria. While Caudoviricetes (realm Duplodnaviria) represented more than 90% of the relative abundance of viruses found in hydrocarbon-contaminated soils, this class represented less than 62% of the viruses of uncontaminated soils. Most viral hosts detected in King George Island soils belonged to hydrocarbon-degrading bacterial genera from the phyla Pseudomonadota and Actinomycetota. Hydrocarbon contamination resulted in the enrichment of well-characterized viruses at the expense of previously uncharacterized viral taxa, which were predominantly detected in non-contaminated soils. Among them, Gordonia-related Stormageddonvirus was the most abundant viral entity identified in King George Island soil. Viral auxiliary metabolic genes (AMGs) associated with nitrogen and phosphate cycles were found in different Caudoviricetes-related contigs. Our results further indicate that Caudoviricetes abundance is correlated with the carbon: phosphate (C:P) ratio in King George Island soils. We propose the Caudoviricetes may actively contribute to microbial competition for phosphorus in hydrocarbon-contaminated soils. These findings shed light on the intricate interplay between viruses, microbial hosts, and environmental contamination in Antarctic soils.}, } @article {pmid40810220, year = {2025}, author = {Ni, Z and Yanxi, C and Lianqun, J and Xinya, LI and Yixin, MA}, title = {Huayu Qutan formula can improve platelet aggregation in acute coronary syndrome rats by regulating gut microbes to drive trimethylamine/flavin containing monooxygenase 3/trimethylamine N-oxide pathway.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {45}, number = {4}, pages = {747-758}, pmid = {40810220}, issn = {2589-451X}, support = {82104841//National Natural Science Foundation of China Project: based on the Theory of "the Heart is in Harmony with the Small Intestine" to Explore the Influence and Mechanism of Gut Microbes on High Platelet Reactivity of Acute Coronary Syndrome with Phlegm and Blood Stasis Syndrome/ ; L202039//Education Department of Liaoning Province Young Science and Technology Talents "Seedling" Project: to Explore the Effect and Mechanism of Huayu Qutan Formula on Platelet Function in Acute Coronary Syndrome Patients with Phlegm and Blood Stasis Syndrome after Percutaneous Coronary Intervention based on Intestinal Microbiome/ ; }, mesh = {Animals ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Drugs, Chinese Herbal/administration & dosage ; Male ; *Platelet Aggregation/drug effects ; *Acute Coronary Syndrome/drug therapy/microbiology/metabolism/physiopathology ; *Oxygenases/metabolism/genetics ; Rats, Sprague-Dawley ; Bacteria/classification/isolation & purification/genetics/metabolism/drug effects ; Humans ; }, abstract = {OBJECTIVE: To investigate the effects of gut microbes regulation of the trimethylamine (TMA)/flavin containing monooxygenase 3 (FMO3)/trimethylamine N-oxide (TMAO) pathway on platelet aggregation in acute coronary syndrome (ACS) rats and the intervention of Huayu Qutan formula.

METHODS: The ACS rats with syndrome of phlegm and blood stasis rats were established. Platelet, platelet aggregation, platelet activation markers and TMA/FMO3/ TMAO pathway were detected. Metagenomics technology was employed to analyze the characteristics of the gut microbiota.

RESULTS: Huayu Qutan formula and gut microbes could inhibit high platelet reactivity and regulate the TMA/ FMO3/TMAO pathway. The dominant bacteria in ACS rats including but not limited to the major phyla, Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, also including some low abundance phyla, Fusobacteria, Verrucomicrobia, Spirochaetes, and Deferribacteres. The dominant bacteria in the Huayu Qutan formula group were Synergistetes, Deferribacteres, Deferribacteraceae, Faecalibacterium and Mucispirillum. In the Huayu Qutan formula combined with fecal bacteria enema group, the dominant bacteria were Verrucomicrobia, Verrucomicrobiae, Akkermansia and Verrucomicrobium. These gut microbiota were correlated with pathways such as Riboflavin metabolism and Arachidonic acid metabolism.

CONCLUSION: Huayu Qutan formula may prevent ACS by modulating gut microbes Synergistetes, Faecalibacterium and Allobaculum, regulating the iron metabolism of Deferribacteres, and driving the TMA/FMO3/TMAO pathway to regulate gut microbiota function, and improving platelet aggregation. Akkermansia may serve as a promising probiotic, which could drive TMA/FMO3/ TMAO pathway to regulate Arachidonic acid metabolism to improve platelet aggregation. The findings of this study provide a theoretical basis for the theory of "the heart is connected with the small intestine".}, } @article {pmid40808637, year = {2025}, author = {Ferhaoui, N and Sebaihia, M and Sekizuka, T and Kuroda, M}, title = {Shotgun Metagenomic Investigation of the Microbiome in Diabetic Foot Infections Compared to Healthy Skin.}, journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society}, volume = {33}, number = {4}, pages = {e70074}, doi = {10.1111/wrr.70074}, pmid = {40808637}, issn = {1524-475X}, support = {//Algerian Ministry of Higher Education and Scientific Research (DGRSDT/MESRS)/ ; JP23fk0108666j0401//Research Program on Emerging and Reemerging Infectious Diseases of the Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Diabetic Foot/microbiology ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; *Skin/microbiology ; Metagenomics ; Aged ; Adult ; Wound Healing ; }, abstract = {Diabetic foot infection (DFI) is a major complication of diabetes, causing significant morbidity and mortality. Host factors and microorganisms in DFI can disrupt healing processes, leading to chronic, non-healing wounds. The aim of this study was to characterise the microbiome of DFIs and contralateral healthy foot skin (CHFS). Thirty-two diabetic patients were enrolled in this study. Samples were obtained from DFIs and CHFS from the same patient. The microbiome was profiled using metagenomic shotgun sequencing. All the samples were polymicrobial, with a predominance of the obligate anaerobes belonging to Bacteroidetes in PEDIS 4. While PEDIS 3 and 2 were dominated by Proteobacteria. CHFS showed similar bacterial composition across all grades of severity, and the most abundant genera detected were Corynebacterium, Staphylococcus, Pseudomonas, and Cutibacterium. The CHFS was more diverse than DFIs in PEDIS 3 and 4. However, DFIs and CHFS in PEDIS 2 present similar diversity. In addition, DFIs of this grade exhibited a high proportion of Corynebacterium as well as CHFS. PCoA analysis demonstrated that the community structure of DFIs was different from that of CHFS, with Prevotella, Bacteroides, and Porphyromonas the main contributors to the clustering. Neighbour-Net analyses revealed that DFIs exhibited lower diversity compared to CHFS and harboured a more homogeneous dominant bacterial community. Our study revealed a high abundance of obligate anaerobes, including Bacteroides, Prevotella, Morganella, and Porphyromonas, in more severe infections; along with a decrease in microbial diversity. Additionally, there was a decrease in the abundance of key bacteria from the normal skin microbiota.}, } @article {pmid40797468, year = {2025}, author = {Guo, T and Chang, L and Huang, PW and Yao, JP and Zhang, YC and Ren, CY and Bao, CQ}, title = {Investigating the mediating effect of plasma metabolites on the gut microbiome in influencing Behçet disease: A multi-omics validated Mendelian randomization study.}, journal = {Medicine}, volume = {104}, number = {32}, pages = {e42698}, pmid = {40797468}, issn = {1536-5964}, support = {Z202213//Wuxi Municipal Health Commission's research project/ ; }, mesh = {Humans ; *Behcet Syndrome/microbiology/blood/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; Multiomics ; }, abstract = {Although an established correlation between gut microbiota (GM) and Behçet syndrome exists, the potential mediating involvement of plasma metabolites remains unclear. Using the most recent statistical data from genome-wide association studies conducted in 2024, we investigated the causal relationships between 473 GM taxa, 233 circulating metabolites, and Behçet syndrome (Behçet disease [BD]) through a 2-sample Mendelian randomization approach. This analysis was further supported by incorporating transcriptome and metagenomic data related to BD. A 2-step methodology was employed to evaluate the extent to which the effect of GM on BD is mediated through plasma metabolites. These results were subsequently validated in a separate validation set. Our Mendelian randomization results demonstrated correlations between various GM and the risk of Behçet syndrome. The potential link between GM and BD risk may be mediated through plasma circulating metabolite levels. Specifically, for every standard deviation, an increase in the abundance of Turicibacter sp001543345 was correlated with a 403% increase in BD risk (odds ratio : 5.03 [95% confidence interval, 1.77-14.25]). Meanwhile, the cholesteryl esters to total lipids ratio in large very low-density lipoprotein and the total cholesterol to total lipids ratio in very large very low-density lipoprotein increased by 4%. The proportion of indirect effects is 3.026% and 3.338%, respectively. Our study established a causal link between distinct GM and BD and quantified the proportion of effects mediated through plasma metabolites. These findings provide further insights for the treatment of BD.}, } @article {pmid40794845, year = {2025}, author = {Heber, K and Tian, S and Betancurt-Anzola, D and Koo, H and Bisanz, JE}, title = {StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {8}, pages = {}, pmid = {40794845}, issn = {1367-4811}, support = {R00 AI147165/AI/NIAID NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Software ; *Metagenomics/methods ; *Microbiota/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.

RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification.

Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.}, } @article {pmid40789238, year = {2025}, author = {Geng, B and Zhu, C and Cui, Z and Chen, Y and Zhang, Q and Shi, H and Min, L and Zhu, S and Zhang, W and Zhao, M and Zhang, S and Xu, J}, title = {Maslinic acid alleviates ulcerative colitis by inhibiting the colitis-aggravating pathogen Clostridium perfringens and modulating gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {146}, number = {}, pages = {157144}, doi = {10.1016/j.phymed.2025.157144}, pmid = {40789238}, issn = {1618-095X}, mesh = {Animals ; *Clostridium perfringens/drug effects/pathogenicity ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Mice ; *Triterpenes/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; Male ; Humans ; Dextran Sulfate ; Oleanolic Acid/analogs & derivatives ; }, abstract = {BACKGROUND: Ulcerative colitis (UC), a prevalent form of inflammatory bowel disease, continues to pose therapeutic challenges due to the limitations of conventional drugs and their inability to prevent relapse. Emerging evidence highlights the crucial role of gut microbiota dysbiosis in UC pathogenesis, yet our understanding of specific harmful microbes and their contributions to disease development remains limited.

PURPOSE: This study aims to (1) investigate the therapeutic potential of maslinic acid (MA), a food-derived natural compound, in colitis mice models; (2) elucidate the previously underestimated pathogenic role of Clostridium perfringens in UC development; and (3) reveal the molecular mechanisms underlying both C. perfringens pathogenesis and MA-mediated protection.

METHODS: We examined the therapeutic effect of MA using DSS-induced colitis model and performing metagenomic sequencing; elucidated the pathogenic role of C. perfringens using GMrepo database, clinical stool samples, and in vivo infection models. Additionally, we revealed its mechanism using inhibitors and markers of various cell death and inflammation pathways. The bactericidal effect of MA on C. perfringens was studied through in vitro experiments and two in vivo colitis models.

RESULTS: MA alleviates DSS-induced colitis and restores gut microbiota. C. perfringens is enriched following DSS administration while significantly decreased after treatment with MA. C. perfringens contributes to the development of colitis and induces ZBP1-mediated PANoptosis in intestinal epithelial cells, while stimulates inflammation through NOD2 activation. MA has direct bactericidal activity against C. perfringens through ROS induction. It can almost completely rescue the exacerbation of colitis-related pathological and physiological phenotypes caused by C. perfringens in two mice colitis models.

CONCLUSIONS: Our study reveals that MA effectively mitigates DSS-induced colitis by inhibiting the colitis-aggravating pathogen C. perfringens and modulating gut microbiota. Furthermore, it elucidates the previously underestimated role and mechanism of C. perfringens in the development of UC. It also highlights the therapeutic potential of MA in preventing and treating UC, particularly in patients who are C. perfringens positive.}, } @article {pmid40767409, year = {2025}, author = {Liu, WS and Liu, CD and Liu, C and van der Ent, A and Cao, Y and Chao, YQ and Qiu, RL and Tang, YT}, title = {Microbial Phosphate Solubilization Promotes Rare Earth Element Accumulation in the Hyperaccumulator Dicranopteris linearis from China.}, journal = {Environmental science & technology}, volume = {59}, number = {32}, pages = {17092-17102}, doi = {10.1021/acs.est.5c05746}, pmid = {40767409}, issn = {1520-5851}, mesh = {China ; Rhizosphere ; *Phosphates/metabolism ; Soil/chemistry ; *Metals, Rare Earth/metabolism ; Phosphorus ; Soil Microbiology ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Plant and rhizosphere soil samples of the rare earth element (REE) hyperaccumulator plant Dicranopteris linearis were collected across tropical and subtropical China to elucidate how rhizosphere microbiota drive soil REE solubilization and accumulation in this species. The results show that this facultative REE hyperaccumulator species grows under severe phosphorus deficiency conditions, with soil available phosphorus concentrations ∼2 mg kg[-1] and a leaf nitrogen-to-phosphorus ratio >20. The core rhizosphere microbiota comprise 111 OTUs (occupancy >95%, relative abundance >0.1%), with community structure primarily correlated with soil phosphorus availability, rather than with geographical location or climatic variables. Foliar phosphorus and REE concentrations are positively associated with soil total phosphorus concentrations and glucose dehydrogenase (GCD) gene abundance─a key biomarker of microbial phosphate solubilization activity─but exhibit no significant association with soil available phosphorus or soil extractable REE concentrations. Combined 16S rRNA sequencing and metagenomic analyses further reveal abundant phosphate-solubilizing microbes within the core microbiome. These results show that REE mineral weathering in the rhizosphere soil and subsequent accumulation in D. linearis are side effects of phosphate solubilization promoted by the rhizosphere microbiome under phosphorus deficiency conditions.}, } @article {pmid40742667, year = {2025}, author = {Liang, M and Wu, WJ and Li, L and Qin, H and Li, SN and Zheng, GL and Hou, DM and Huang, Q and Cheng, L and Jie, HQ and Lu, JR and He, JC and Yang, J and Wei, W}, title = {Characteristics of the microbiota in the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic.}, journal = {World journal of pediatrics : WJP}, volume = {21}, number = {8}, pages = {836-845}, doi = {10.1007/s12519-025-00953-z}, pmid = {40742667}, issn = {1867-0687}, support = {81800903//National Natural Science Foundation of China/ ; 82171135//National Natural Science Foundation of China/ ; 82371140//National Natural Science Foundation of China/ ; 81970881//National Natural Science Foundation of China/ ; 82271160//National Natural Science Foundation of China/ ; 21Y31900504//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 2024YFC2511100//National Key R&D Program of China/ ; }, mesh = {Humans ; *COVID-19/epidemiology ; *Nasopharynx/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; Male ; Female ; Child ; SARS-CoV-2 ; Pandemics ; Child, Preschool ; Infant ; }, abstract = {BACKGROUND: Microbial colonization in the nasopharynx and nasal cavity plays a defensive role in children. The coronavirus disease 2019 (COVID-19) pandemic may have an influence on the nasopharynx and nasal cavity microbiota. This study aimed to identify and compare the microbiota in the nasopharynx and nasal cavity before and during the COVID-19 pandemic in a healthy pediatric population.

METHODS: Separate mucosal swabs were collected from the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic. A 16S ribosomal RNA-based metagenomic approach was employed to characterize and analyze alterations in the nasopharyngeal and nasal microbiota to determine whether isolation measures, such as mask wearing, influence microbial ecology.

RESULTS: The richness and diversity of the nasopharyngeal and nasal microbiota decreased during the COVID-19 pandemic compared with before the pandemic. Firmicutes and Proteobacteria were the most abundant phyla in the nasopharyngeal and nasal microbiota, respectively, both before and during the pandemic. Corynebacterium and Moraxella were the dominant genera in the nasopharyngeal and nasal microbiota during the COVID-19 pandemic, whereas Pseudomonas and Corynebacterium were dominant before the pandemic. Compared with pre-pandemic conditions, microbial colonization differed significantly for Cyanobacteria/Chloroplast and Bacteroidetes in the nasopharynx and for Planctomycetes in the nasal cavity during the COVID-19 pandemic.

CONCLUSIONS: This study revealed a lower microbiota diversity during COVID-19, possibly accompanied by microbiota dysbiosis, increased risk of respiratory infections and inflammatory responses in healthy children. This study underscores the importance of reestablishing microbiota balance and highlights the need for personalized treatment and prophylactic strategies in routine public health practice. Supplementary file3 (MP4 150533 KB).}, } @article {pmid40730159, year = {2025}, author = {Che, Y and Han, J and Harkins, CP and Hou, P and Conlan, S and Deming, C and Amirkhani, A and Bingham, MA and Holmes, CJ and Englander, H and Shen, Z and , and Castelo-Soccio, L and Dimitrova, D and Kanakry, JA and Bergerson, JRE and Notarangelo, LD and Pittaluga, S and Zhao, C and Dell'Orso, S and Pai, SY and Hickstein, DD and Holland, SM and Brownell, I and Nagao, K and Gonzalez, CE and Shah, NN and Freeman, AF and Su, HC and Segre, JA and Kong, HH}, title = {Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation.}, journal = {Cell host & microbe}, volume = {33}, number = {8}, pages = {1412-1427.e5}, pmid = {40730159}, issn = {1934-6069}, support = {ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; ZIA AR041217/ImNIH/Intramural NIH HHS/United States ; ZIA BC011558/ImNIH/Intramural NIH HHS/United States ; ZIA BC010938/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation ; *Skin/microbiology/virology/immunology ; *Microbiota/immunology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Adult ; Young Adult ; Metagenomics ; Child ; Adolescent ; Bacteria/classification/genetics/isolation & purification ; Child, Preschool ; Skin Microbiome ; }, abstract = {The human skin microbiome is intricately intertwined with host immunity. While studies have elucidated microbial influences on immunity, understanding how immune alterations modulate this equilibrium remains limited. We investigated the dual impact of immune deficiency and hematopoietic stem cell transplantation (HSCT) on the skin microbiome in 24 patients with dedicator of cytokinesis 8 (DOCK8) deficiency, a rare inborn error of immunity. Analyzing 590 metagenomic and 534 16S rDNA sequencing samples across eight skin sites, we observed disrupted microbiota pre-HSCT (median eukaryotic viruses 67.6% vs. 0.04% in controls), with extremely diverse human papillomaviruses (HPVs) and polyomaviruses-including oncogenic viruses. Specific bacterial species markedly changed, including decreased Staphylococcus aureus post-HSCT. DNA eukaryotic viruses dramatically decreased (79.7% ± 28.3% to 4.9% ± 8.6%; p < 0.01) 12 months post-HSCT. Recovered microbial communities remained relatively stable through 1-year follow-up with clearance of oncogenic HPV and no convergence with transplant donors. These results highlight the immune system's critical role in restoring microbial balance and skin health.}, } @article {pmid40719460, year = {2025}, author = {Tang, J and Baker, JL}, title = {The salivary virome during childhood dental caries.}, journal = {mSphere}, volume = {10}, number = {8}, pages = {e0019825}, pmid = {40719460}, issn = {2379-5042}, support = {R00-DE029228/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Dental Caries/virology/microbiology ; *Saliva/virology ; *Virome ; Child ; Male ; Female ; Child, Preschool ; Metagenomics ; Metagenome ; Genome, Viral ; *Viruses/classification/genetics/isolation & purification ; Bacteriophages/genetics/classification ; Bacteria ; Microbiota ; }, abstract = {While many studies have examined the bacterial taxa associated with dental caries, the most common chronic infectious disease, little is known about the caries-associated virome. In this study, the salivary viromes of 21 children with severe caries (>2 dentin lesions) and 23 children with healthy dentition were examined. A total of 2,485 viral metagenome-assembled genomes (vMAGs) were identified, binned, and quantified from the metagenomic assemblies. These vMAGs were mostly phages and represented 1,865 unique species-level viral operational taxonomic units (vOTUs), of which 478 appear to be novel. The metagenomes were also queried for all 3,858 unique species-level vOTUs of DNA viruses with a human host on NCBI Virus; however, all but Human betaherpesvirus 7 were at very low abundance in the saliva. The oral viromes of the children with caries exhibited significantly different beta diversity compared to the oral virome of the children with healthy dentition; several vOTUs predicted to infect Haemophilus and Neisseria were strongly correlated with health, and five vOTUs predicted to infect Saccharibacteria, Prevotella, and Veillonella were correlated with caries. Co-occurrence analysis indicated that the phage typically co-occurred with both their predicted hosts and with bacteria that were themselves associated with the same disease status. Overall, this study provided the sequences of 35 complete or nearly complete novel oral phages and illustrated the potential significance of the oral virome in the context of dental caries, which has been largely overlooked. This work represents an important step toward the identification and study of phage therapy candidates that treat or prevent caries pathogenesis.IMPORTANCEDental caries is the most common chronic infectious disease worldwide and is caused by dysbiosis of the oral microbiome featuring an increased abundance of acid-tolerant, acid-producing, and biofilm-forming bacteria. The oral microbiome also contains viruses; however, very little is known about the caries-associated virome. In this study, the salivary virome of children with severe caries was compared to the salivary virome of children with healthy dentition. The metagenomes contained a total of 1,865 unique species-level viral operational taxonomic units (vOTUs), of which 478 appeared to be novel. The viromes from the children with caries were significantly different than the viromes from the children with healthy teeth, and several health- and disease-associated vOTUs were identified. This study illustrated the potential importance of the oral virome in the context of dental caries and serves as a step towards a better understanding of oral inter-kingdom interactions and identification of potential phage-based caries therapeutics.}, } @article {pmid40633350, year = {2025}, author = {Huang, C and Wang, T and Chen, W and Wang, J and Cui, M and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Xu, L and Fang, H}, title = {Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139157}, doi = {10.1016/j.jhazmat.2025.139157}, pmid = {40633350}, issn = {1873-3336}, mesh = {*Manure ; *Soil Microbiology ; Animals ; Sheep ; *Anti-Bacterial Agents/pharmacology ; *Brassica rapa ; *Drug Resistance, Microbial/genetics ; Agriculture ; Bacteria/genetics/drug effects ; Microbiota ; Soil/chemistry ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.}, } @article {pmid40614422, year = {2025}, author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S}, title = {The invisible threats of sunscreen as a plastic co-pollutant: Impact of a common organic UV filter on biofilm formation and metabolic function in the nascent marine plastisphere.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139103}, doi = {10.1016/j.jhazmat.2025.139103}, pmid = {40614422}, issn = {1873-3336}, mesh = {*Sunscreening Agents/toxicity ; *Biofilms/drug effects/growth & development ; *Water Pollutants, Chemical/toxicity ; *Plastics ; Bacteria/drug effects/genetics/metabolism ; Polyethylene ; Ultraviolet Rays ; Microbiota/drug effects ; Cinnamates ; }, abstract = {Plastic debris in marine environments serves as a substrate for microbial colonisation, forming biofilms known as 'plastispheres'. Also accumulated on plastic debris are co-pollutants including UV-protective organic UV-filters from sunscreens, which likely interact with this niche through their lipophilicity. Despite their widespread use and environmental accumulation, the influence of UV-filters on plastisphere composition and function has never been investigated. This study therefore investigates, for the first time, how co-pollution - specifically by an organic UV-filter - impacts the composition and function of marine plastisphere communities. To achieve this, low-density polyethylene (LDPE) was incubated with marine microbial communities for six days to cultivate a nascent plastisphere, which was then exposed to 5 mg/L of EthylHexyl MethoxyCinnamate (EHMC); the most used organic UV-filter in sunscreens, and a prevalent marine pollutant. Metagenomic analyses revealed that EHMC favoured the growth of bacterial generalists Pseudomonas and Psychromonas while reducing pollutant-degrading genera like Marinomonas. Analysis of 3070 proteins revealed a consistent upregulation of proteins used for biofilm maintenance by Pseudomonas with EHMC exposure, including the considerable upregulation of outer membrane porin F (OprF) which regulates exopolymeric substance (EPS) production. Additionally, proteins thought to indicate a shift from aerobic to anaerobic respiration were frequently expressed after exposure to EHMC. This may have selected against the obligate aerobes Marinomonas and Pseudoalteromonas, contributing to the observed shift in community composition. These findings underscore the importance of considering chemical co-pollutants in plastisphere research as we now begin to discover how ecologically significant, and potentially harmful microbial genera are affected by this interaction.}, } @article {pmid40586263, year = {2025}, author = {Bonham, KS and Margolis, ET and Fahur Bottino, G and Sobrino, AC and Patel, F and McCann, S and Zieff, MR and Miles, M and Herr, D and Davel, L and Bosco, C and , and Huttenhower, C and Pini, N and Alexander, DC and Jones, DK and Williams, SCR and Amso, D and Gladstone, M and Fifer, WP and Donald, KA and Gabard-Durnam, LJ and Klepac-Ceraj, V}, title = {Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy.}, journal = {mBio}, volume = {16}, number = {8}, pages = {e0083525}, pmid = {40586263}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; Evoked Potentials, Visual ; Male ; Female ; Neuronal Plasticity ; Longitudinal Studies ; *Visual Cortex/growth & development/physiology ; Electroencephalography ; Brain/growth & development ; }, abstract = {Infancy is a time of elevated neuroplasticity supporting rapid brain and sensory development. The gut microbiome, also undergoing extensive developmental changes in early life, may influence brain development through the metabolism of neuroactive compounds. Here, we leverage longitudinal data from 194 South African infants across the first 18 months of life to show that microbial genes encoding enzymes that metabolize molecules playing a key role in modulating early neuroplasticity are associated with visual cortical neurodevelopment, measured by the Visual-Evoked Potential (VEP). Neuroactive compounds included neurotransmitters GABA and glutamate, the amino acid tryptophan, and short-chain fatty acids involved in myelination, including acetate and butyrate. Microbial gene sets around 4 months of age were strongly associated with the VEP from around 9-14 months of age and showed more associations than concurrently measured gene sets, suggesting that microbial metabolism in early life may affect subsequent neural plasticity and development.IMPORTANCEOver the past decade, extensive research has revealed strong links between the gut microbiome and the brain, at least in adults or those with neuropsychiatric disorders. This study explores how these associations emerge in early development using a longitudinal sample of 194 infants with repeated microbiome metabolism and electroencephalography (EEG) measures during the critical early period of visual cortex neuroplasticity. We examined microbial genes encoding enzymes for neuroactive compounds (e.g., GABA, glutamate, tryptophan, and short-chain fatty acids) and their association with the visual-evoked potential (VEP). Genes from 4-month stool samples strongly correlated with VEP features between 9 and 14 months, suggesting that early microbial metabolism influences later visual neurodevelopment. These prospective associations were more numerous than the concurrent ones. Our findings suggest that early gut microbiome metabolic potential plays a crucial role in shaping neural plasticity and visual neurodevelopment.}, } @article {pmid40580733, year = {2025}, author = {Du, S and Tang, H and Wang, Z and Chen, H and Fang, X and Sun, J and Niu, Z and Liu, Y and Hu, Y and Su, W and Zhang, Z and Prapamontol, T and Nakayama, SF and Huang, J and Norback, D and Wu, Q and Tan, Y and Zhao, Z}, title = {Children's home environments as reservoirs of antimicrobial resistance: Divergent urban-rural risks from antibiotic resistance genes and pathogens.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139053}, doi = {10.1016/j.jhazmat.2025.139053}, pmid = {40580733}, issn = {1873-3336}, mesh = {Humans ; China ; Child ; Rural Population ; *Drug Resistance, Microbial/genetics ; *Dust/analysis ; Urban Population ; Housing ; Microbiota ; Genes, Bacterial ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance genes(ARGs) and pathogens pose a global health challenge, particularly for vulnerable children. However, limited knowledge is on their existence in home environments where children spend majority of time, even less on urban-rural differences. We collected settled dust from children's homes in urban(n = 31) and rural (n = 34) areas of Shanghai, China, and analyzed microbiomes, ARGs and pathogens through metagenomic sequencing. Home dust microbial compositions differed significantly between urban and rural environment. ARGs were widely detected in home environment (rural:758 subtypes; urban:733). Significant urban-rural differences were also observed in ARGs and pathogens composition, diversity, co-occurrence patterns, assembly processes and drivers. Specifically, rural dust was enriched with more differentially abundant ARG subtypes. Urban dust was enriched with clinically critical multidrug-resistant pathogens (e.g. Acinetobacter baumannii), contrasting with rural areas enriched in plant-associated pathogens. Stochastic processes dominated the assembly of ARGs and pathogens, while environmental factors partially explained their variations. Temperature was positively associated with total ARG abundance in both areas. Residential greenness had a positive relationship with ARG abundance in rural but negative in urban settings. Our findings indicated children's homes as reservoirs of antimicrobial resistance, urging vigilance against rural ARG enrichment and urban multidrug-resistant pathogen risks for pediatric health.}, } @article {pmid40570627, year = {2025}, author = {Li, YQ and Zhang, CM and Ma, H and Shao, KJ and Yuan, PH and Jiang, HY}, title = {Antiallergic drugs drive the alteration of microbial community and antibiotic resistome in surface waters: A metagenomic perspective.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139028}, doi = {10.1016/j.jhazmat.2025.139028}, pmid = {40570627}, issn = {1873-3336}, mesh = {*Anti-Allergic Agents/pharmacology ; *Water Pollutants, Chemical/toxicity/pharmacology ; *Microbiota/drug effects ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics ; *Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome/drug effects ; }, abstract = {Antiallergic drugs (AADs) are emerging contaminants of global concern due to their environmental persistence and potential ecological impacts. This study investigated the effects of seven AADs (chlorpheniramine, diphenhydramine, cetirizine, loratadine, desloratadine, sodium cromoglicate and calcium gluconate) at environmentally relevant concentrations on antibiotic resistome and bacterial community structures in water using microcosm experiments and metagenomic sequencing. The results showed that AADs increased the abundance of antibiotic-resistant bacteria (ARB) by 1.24- to 7.78-fold. Community structure shifts indicated that chlorpheniramine, diphenhydramine, and cetirizine promoted Actinobacteria (e.g., Aurantimicrobium), while the other four AADs favored Proteobacteria (e.g., Limnohabitans). AADs also significantly altered the relative abundance of antibiotic resistance genes (ARGs), with Actinobacteria and Proteobacteria identified as key ARB components and potential hosts of ARGs (e.g., evgS, mtrA, RanA). Host analysis showed ARGs were primarily carried by Actinobacteria (e.g., Aurantimicrobium) under chlorpheniramine, diphenhydramine, and cetirizine exposure, but by Proteobacteria (e.g., Limnohabitans) under the other four AADs. Furthermore, AADs facilitated the horizontal transfer of ARGs (e.g., evgS) within microbial communities, contributing to antibiotic resistance dissemination. This study highlights the ecological risks of AADs in promoting antibiotic resistance spread and provides new insights into their impact on microbial communities and resistome dynamics in aquatic environments.}, } @article {pmid40527211, year = {2025}, author = {Ghosh, S and Nath, S and Chakraborty, A and Bhowmick, S and Majumdar, KK and Mukherjee, S and Pramanik, S}, title = {Long-term arsenic exposure perturbs gut microbial diversity, composition and predicts metabolic dysregulation.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138836}, doi = {10.1016/j.jhazmat.2025.138836}, pmid = {40527211}, issn = {1873-3336}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Arsenic/toxicity ; Adult ; Male ; India ; Feces/microbiology ; Female ; Bacteria/genetics/drug effects/classification ; Middle Aged ; }, abstract = {The present study documents significant alterations in human gut microbial composition in arsenic exposed populations of West Bengal, India through amplicon sequencing of human stool metagenomic DNA. A notable reduction in α-diversity underscored a reduced species richness and an altered predominance. β- diversity analysis revealed prominent inter-individual differences. Among the 26 phyla detected, significant perturbation was noted in Bacteroidetes, Actinobacteria, Proteobacteria, and Firmicutes. Species analysis identified significant increase in Bifidobacterium adolescentis, B.longum, Blautia luti, B.wexlerae, Clostridium saudiense, Romboutsia timonensis and Streptococcus salivarius whereas members of Faecalibacterium prausnitzii, Megasphaera elsdenii, Prevotella copri and P. stercorea were found to be highly diminished due to As stress. PICRUSt analysis predicted significant upregulation (pT-test< 0.05) in gene families associated with carbohydrate, amino acid, nucleotide and lipid metabolism along with fermentation and secondary metabolite/ vitamin synthesis pathways in exposed group confirmed through Linear Discriminant Analysis. B.longum, B.luti and S.salivarius were found to be associated with obesity and ulcerative colitis. Network interactions were also characterized with major disruptions in keystone species interaction. The major findings of this study shall drive future studies like community-based metagenomics, metabolomics and in-vitro microbial verifications for designing of microbial therapeutics targeting gut health to combat the harmful impact of As exposure.}, } @article {pmid40852940, year = {2025}, author = {Philip, M and Nilsen, T and Majaneva, S and Pettersen, R and Stokkan, M and Ray, JL and Keeley, N and Rudi, K and Snipen, LG}, title = {A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70036}, doi = {10.1111/1755-0998.70036}, pmid = {40852940}, issn = {1755-0998}, support = {320076//Norges Forskningsråd/ ; }, abstract = {The Oxford Nanopore Technologies (ONT) sequencing platform is compact and efficient, making it suitable for rapid biodiversity assessments in remote areas. Despite its long reads, ONT has a higher error rate compared to other platforms; necessitating high-quality reference databases for accurate taxonomic assignments. However, the absence of targeted databases for underexplored habitats, such as the seafloor, limits ONT's broader applicability for exploratory analysis. To address this, we propose an approach for building environmentally targeted databases to improve 16S rRNA gene (16S) analysis using Oxford Nanopore Technologies (ONT), using seafloor sediment samples from the Norwegian coast as an example. We started by using Illumina short-read data to create a database of full-length or near full-length 16S sequences from seafloor samples. Initially, amplicons are mapped to the SILVA database, with matches added to our database. Unmatched amplicons are reconstructed using METASEED and Barrnap methodologies with amplicon and metagenome data. Finally, if the previous strategies did not succeed, we included the short-read sequences in the database. This resulted in AQUAeD-DB, which contains 14,545 16S sequences clustered at 95% identity. Comparative database analysis reveals that AQUAeD-DB provides consistent results for both Illumina and Nanopore read assignments (median correlation coefficient: 0.50), whereas a standard database showed a substantially weaker correlation. These findings also emphasise its potential to recognise both high and low abundance taxa, which could be key indicators in environmental studies. This work highlights the necessity of targeted databases for environmental analysis, especially for ONT-based studies, and lays the foundations for future extension of the database.}, } @article {pmid40825123, year = {2025}, author = {Park, JD and Lee, SR and Dhennezel, C and Taylor, N and Dame, A and Kadoki, M and Pishchany, G and Graham, DB and Xavier, RJ and Seyedsayamdost, MR}, title = {Elucidating the role of Campylobacter concisus-derived indole metabolites in gut inflammation and immune modulation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {34}, pages = {e2514071122}, doi = {10.1073/pnas.2514071122}, pmid = {40825123}, issn = {1091-6490}, support = {2023A004123//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; }, mesh = {*Indoles/metabolism ; Animals ; *Gastrointestinal Microbiome/immunology ; *Campylobacter/metabolism/immunology ; Mice ; *Inflammation/immunology/microbiology/metabolism ; Humans ; Macrophages/immunology ; Cytokines/metabolism ; Mice, Inbred C57BL ; Inflammatory Bowel Diseases/microbiology/immunology ; }, abstract = {The gut microbiota plays a pivotal role in maintaining human health with dysbiosis linked to a variety of diseases. Metagenome sequencing and robust statistical analysis have linked specific strains, including the gut bacterium Campylobacter concisus, to Crohn's disease and ulcerative colitis, together known as inflammatory bowel disease (IBD). However, the roles of this and other strains in disease progression remain to be investigated. Herein, we assess the contribution of C. concisus secondary metabolites to inflammation. Through untargeted metabolomics, we identified a diverse array of nineteen indole-containing metabolites produced by C. concisus, including trisindoline, previously isolated from a marine bacterium. Collectively, these metabolites modulate inflammatory responses by significantly inducing the release of proinflammatory cytokines interleukin (IL)-1β, IL-6, IL-8, and MCP-1. The metabolites act through the aromatic hydrocarbon receptor arylhydrocarbon receptor and in vivo intravital imaging revealed a marked increase in the recruitment and activation of immune cells, specifically neutrophils and macrophages, following the administration of trisindoline. Several indole metabolites also exhibited antimicrobial activity against commensal strains that facilitate a proper immune response. Our study provides a possible rationale for the association of C. concisus with IBD and underscores the complex interplay between gut bacteria and host immunity. The identification of indole-derived secondary metabolites as key modulators of inflammation offers new avenues for therapeutic intervention.}, } @article {pmid40817325, year = {2025}, author = {Star-Shirko, B and Pangga, GM and McKenna, A and Corcionivoschi, N and Richmond, A and Ijaz, UZ and Gundogdu, O}, title = {Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {355}, pmid = {40817325}, issn = {1756-0500}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Cecum/microbiology ; *Intestine, Large/microbiology ; Metagenome ; }, abstract = {OBJECTIVES: Although taxonomic variations in chicken gut microbiota have been previously documented, their functional capacity remain poorly understood. To gain a better understanding, we incorporated whole genome shotgun metagenomics to analyse microbial communities of two different organs: the caeca and the large intestine.

RESULTS: Using 24 samples obtained from the caeca and the large intestine of commercial chickens, we assembled Metagenome-Assembled Genomes (MAGs) and characterise their functional profiles. Afterwards, using 8 samples, we integrated this sequencing data with chicken performance metadata body weight (BW), weight gain, feed intake (FI), feed conversion ratio (FCR) and age. MAGs belonging to specific families were found to be positively associated with changes in performance parameters. Functional analyses suggest changes in nutrient geochemical cycles including hydrogen generation within the carbon-cycle. Furthermore, 108 CAZymes were identified for MAGs belonging to two major families - glycoside hydrolase (GH) and polysaccharide lyase (PL), which are important for breakdown of dietary carbohydrates and fibres. A total of 13 polysaccharide lyases were identified functioning on day 20 with enzymes were specific to organs. Overall, our results provide a deeper understanding of microbial-mediated metabolism concerning key performance parameters in chicken production.}, } @article {pmid40817175, year = {2025}, author = {Yang, JX and Peng, Y and Yang, JJ and Zhang, YH and Dong, Q and Li, QS and Han, XG and Gao, C}, title = {Nitrogen addition alters arbuscular mycorrhizal fungi and soil bacteria networks without promoting phosphorus mineralization in a semiarid grassland.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1229}, pmid = {40817175}, issn = {2399-3642}, mesh = {*Mycorrhizae/genetics/drug effects/metabolism ; *Phosphorus/metabolism ; *Nitrogen/metabolism/pharmacology ; *Soil Microbiology ; *Grassland ; *Bacteria/genetics/metabolism/classification/drug effects ; Soil/chemistry ; Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mycorrhiza interplays with the microbiome in adaptation to environmental fluctuation, yet how arbuscular mycorrhizal fungi (AMF) and the associated microbiome respond to nitrogen addition remains poorly understood. Here, we addressed this gap by conducting amplicon sequencing of AMF 18S rRNA and bacterial 16S rRNA operons, along with shotgun metagenome sequencing, using soil samples collected from a semiarid grassland that has received nitrogen inputs for 11 years at different levels. We found that the nitrogen response of the AMF community was characterized by a negative association whereby increasing nitrogen addition leads to higher beta diversity and lower alpha diversity. Multiple co-inertia analyses revealed a coordinated response of the AMF community, bacterial community, and bacterial functions to nitrogen addition, which as a whole was strongly related to soil phosphorus availability. Besides, through network analysis of AMF with bacteria and bacterial functional genes, we found that nitrogen addition selected Actinobacteria and enriched functions of transporters, amino acid synthesis and metabolism, and replication repair, whereas there was no evidence for the enrichment of phosphorus mineralization functions.}, } @article {pmid40797356, year = {2025}, author = {Rashwan, HH and Ali, MH and Mostafa, MM and Ramadan, R and Mysara, M}, title = {Insights into the tripartite relationship between cervical cancer, human papillomavirus, and the vaginal microbiome: a mega-analysis.}, journal = {Human genomics}, volume = {19}, number = {1}, pages = {89}, pmid = {40797356}, issn = {1479-7364}, mesh = {Humans ; Female ; *Microbiota/genetics ; *Uterine Cervical Neoplasms/microbiology/virology/genetics/pathology ; *Vagina/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Papillomavirus Infections/microbiology/virology/complications/genetics ; Dysbiosis/microbiology ; *Papillomaviridae/pathogenicity/genetics ; Case-Control Studies ; Adult ; Human Papillomavirus Viruses ; }, abstract = {BACKGROUND: Cervical cancer (CC) is the fourth most prevalent malignancy among women worldwide, where 99.7% of the cases are linked to persistent human papillomavirus (HPV) infections. While emerging evidence suggests a role for vaginal microbiome dysbiosis in HPV-driven CC, the specific microbial alterations and their functional implications remain unclear. However, inconsistencies in identifying specific microbial signatures-largely due to heterogeneous study designs, targeted 16S rRNA regions, and data processing methods-have limited the generalizability of existing findings. To address these challenges, we conducted a standardized mega-analysis using a compositionality-aware approach to ensure consistency and minimize technical bias across studies.

RESULTS: Our mega-analysis consolidates findings from five case-control 16S rRNA ampilicon sequencing studies, encompassing 215 samples. Compared to healthy controls, CC patients exhibited significantly higher alpha diversity (Shannon index, p <0.005) and a shift from a Lactobacillus-dominant to a polymicrobial vaginal microbiome. This microbial dysbiosis was characterized by an increased abundance of Porphyromonadaceae, particularly Porphyromonas asaccharolytica, and other anaerobic bacterial species such as Campylobacter ureolyticus, Peptococcus niger, and Anaerococcus obesiensis (FDR <0.05). Functional profiling of the altered microbiome revealed enrichment in pathways associated with chronic inflammation, fatty acid biosynthesis, amino acid metabolism, cellular proliferation, invasion, and metastasis.

CONCLUSIONS: This mega-analysis presents the most methodologically homogeneous study to date of CC-associated vaginal microbiome using publicly available 16S datasets. Our findings not only deepen our understanding of microbial influences on CC but also pave the way for novel diagnostic and therapeutic approaches potentially enhancing patient outcomes in CC care. These insights open new avenues for clinical interventions that extend beyond conventional HPV-centric strategies.}, } @article {pmid40796374, year = {2025}, author = {Pan, S and Du, H and Zheng, R and Zhang, C and Pan, J and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and He, Z and Tian, Y and Jiang, C and Qu, W and Liu, Y and Li, M}, title = {A holistic genome dataset of bacteria and archaea of mangrove sediments.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40796374}, issn = {2047-217X}, support = {2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 92251306//National Natural Science Foundation of China/ ; 92051102//National Natural Science Foundation of China/ ; 92251307//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32200099//National Natural Science Foundation of China/ ; 32070108//National Natural Science Foundation of China/ ; 32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 42303064//National Natural Science Foundation of China/ ; 42430707//National Natural Science Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; KCXFZ20201221173404012//Shenzhen Science and Technology Program/ ; JCYJ20230808105711023//Shenzhen Science and Technology Program/ ; 20220809161641002//Shenzhen Science and Technology Program/ ; SML2023SP218/SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; 2022B002//Shenzhen University/ ; }, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; *Genome, Bacterial ; China ; Microbiota/genetics ; *Genome, Archaeal ; Wetlands ; }, abstract = {BACKGROUND: Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contribute to pivotal ecological functions in mangrove ecosystems. However, the study of mangrove sediment microbiomes is limited.

FINDINGS: Here, we applied metagenome sequencing analysis of microbial communities in mangrove sediments across Southeast China from 2014 to 2020. This genome dataset includes 966 metagenome-assembled genomes with ≥50% completeness and ≤10% contamination generated from 6 groups of samples. Phylogenomic analysis and taxonomy classification show that mangrove sediments are inhabited by microbial communities with high species diversity. Thermoplasmatota, Thermoproteota, and Asgardarchaeota in archaea, as well as Proteobacteria, Desulfobacterota, Chloroflexota, Acidobacteriota, and Gemmatimonadota in bacteria, dominate the mangrove sediments across Southeast China. Functional analyses suggest that the microbial communities may contribute to carbon, nitrogen, and sulfur cycling in mangrove sediments.

CONCLUSIONS: These combined microbial genomes provide an important complement of global mangrove genome datasets and may serve as a foundational resource for enhancing our understanding of the composition and functions of mangrove sediment microbiomes.}, } @article {pmid40794939, year = {2025}, author = {Kannan, EP and Venkatachalam, P and Gopal, J and Sarkaraisamy, P and Muthu, M}, title = {Temporal shift of bacterial communities in poultry litter during the course of broiler chicken rearing: a 16S rRNA-based metagenomic study.}, journal = {Journal of applied microbiology}, volume = {136}, number = {8}, pages = {}, doi = {10.1093/jambio/lxaf199}, pmid = {40794939}, issn = {1365-2672}, support = {//DRDO/ ; }, mesh = {Animals ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics ; India ; DNA, Bacterial/genetics ; *Manure/microbiology ; *Microbiota ; Soil Microbiology ; Phylogeny ; }, abstract = {AIM: To decipher the bacterial community transitions of poultry litter at various time frames over a 6-week rearing cycle in a commercial broiler chicken poultry farm in Marakanam, Tamil Nadu, India.

METHODS AND RESULTS: The bacterial consortia of poultry litter were elucidated using the 16S rRNA-based metagenomic Oxford nanopore sequencing method, followed by taxonomic assignment using the Kraken2 tool. Our findings unveiled the varied dominance patterns of bacteria in poultry litter (P1-P6) with Sphingobacterium sp. 21 (53%) in P1, Amphibacillus xylanus dominated in P2 (∼12%), Oceanimonas sp. GK1 in P3 (∼14%) and P6 (>50%), Anaerococcus prevotii in P4 (∼10%) and Marinobacter hydrocarbonoclasticus (∼15%) in P5. Importantly various bacteria involved in key biogeochemical cycles, including Nitrosomonas eutropha (nitrogen cycle), Bacillus subtilis (phosphorous cycle), and Acidithiobacillus caldus (sulphur cycle) were detected indicating a strong potential of utilizing the poultry litter as an effective biofertilizer. On the other hand, harmful human pathogens, including Mycobacterium tuberculosis, Escherichia coli, Salmonella enterica, and Streptococcus pneumoniae were also detected indicating significant public health concern associated with the application of poultry litter as fertilizer.

CONCLUSIONS: This study offers knowledge to both leverage the usefulness of poultry litter as biofertilizer and to mitigate transmission of harmful pathogens harboured by poultry litter.}, } @article {pmid40782046, year = {2025}, author = {Bradley, ES and Stansky, C and Zeamer, AL and Huang, Z and Cincotta, L and Lopes, A and Potter, L and Fontes, T and Ward, DV and Bucci, V and McCormick, BA and Haran, JP}, title = {The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the emergency department.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2546063}, pmid = {40782046}, issn = {2150-5608}, mesh = {Humans ; Aged ; Emergency Service, Hospital ; Female ; Male ; *Urinary Tract Infections/microbiology/diagnosis/urine ; Aged, 80 and over ; *Microbiota ; *Asymptomatic Infections ; Bacteria/classification/genetics/isolation & purification ; Bacteriuria/microbiology/diagnosis ; Urinalysis ; *Urine/microbiology ; Middle Aged ; }, abstract = {Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion of anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, p < 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance p < 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.}, } @article {pmid40779699, year = {2025}, author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH}, title = {Ecological Roles and Shared Microbes Differentiate the Plastisphere from Natural Particle-Associated Microbiomes in Urban Rivers.}, journal = {Environmental science & technology}, volume = {59}, number = {32}, pages = {17298-17309}, pmid = {40779699}, issn = {1520-5851}, mesh = {*Rivers/microbiology ; *Microbiota ; Microplastics ; Ecosystem ; }, abstract = {The "plastisphere," comprising microbes associated with microplastics (MPs), may have substantial ecological impacts on riverine ecosystems. However, little is known about how the microbiomes associated with anthropogenic MPs compare with those associated with natural particles (NPs) in urban rivers with varying MP pollution levels. We therefore conducted a comparative analysis of the metagenomes associated with MPs and NPs (100-5000 μm) and river water (RW) across 10 urban river systems. Although we found similarities in taxonomic and functional compositions between the microbiomes associated with MPs and NPs, the plastisphere exhibited distinct associations with specialized taxa and life-history strategies. These unique traits enhanced the potential of the plastisphere for complex carbohydrate and plastic degradation, nitrate and nitric oxide reduction, and antibiotic resistance and virulence compared with the NP or RW microbiomes. Furthermore, MPs supported the sharing of unique microbes with the surrounding RW; these shared microbes possessed enhanced horizontal gene transfer capabilities and potentially could disperse traits of the plastisphere into the broader RW microbiomes. This study highlights the distinct ecological roles and shared microbes of the plastisphere, indicating that MP pollution may substantially and uniquely impact the function and health of riverine ecosystems.}, } @article {pmid40763732, year = {2025}, author = {Zhou, Z and Jiang, A and Jiang, X and Hatzios, SK}, title = {Metabolic cross-feeding of a dietary antioxidant enhances anaerobic energy metabolism by human gut bacteria.}, journal = {Cell host & microbe}, volume = {33}, number = {8}, pages = {1321-1332.e9}, doi = {10.1016/j.chom.2025.07.008}, pmid = {40763732}, issn = {1934-6069}, mesh = {Humans ; *Energy Metabolism ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Anaerobiosis ; Ergothioneine/metabolism ; Colorectal Neoplasms/microbiology ; *Bacteria/metabolism ; Bacteroides/metabolism ; *Gastrointestinal Tract/microbiology ; Oxidation-Reduction ; Diet ; Adenosine Triphosphate/biosynthesis ; }, abstract = {The degradation of complex carbohydrates and other macromolecules by human gut bacteria generates metabolites that are used by neighboring microbes for anaerobic respiration. However, it is largely unknown whether cross-feeding of other dietary compounds can drive energy-yielding redox reactions in the gut. We show that gut bacteria from different phyla cross-feed a common dietary antioxidant to produce energy under anaerobic conditions. Clostridium symbiosum encodes ergothionases that transform ergothioneine, a mushroom-derived antioxidant, into the electron acceptor thiourocanic acid (TUA). TUA is reduced by Bacteroides xylanisolvens, increasing bacterial ATP synthesis and growth. Furthermore, TUA is selectively produced and consumed by certain human fecal microbial communities. Consistent with emerging links between intestinal ergothioneine homeostasis and colorectal cancer, ergothionase is significantly enriched in fecal metagenomes from colorectal cancer patients. Together, these results illustrate how commensalistic cross-feeding of an antioxidant nutrient enhances microbial energy metabolism, which may contribute to interpersonal differences in disease risk.}, } @article {pmid40749338, year = {2025}, author = {Le, MH and Lee, HJ and Justine, EE and Tran, THM and Kim, YJ}, title = {Bacillus velezensis GV1 polysaccharides enhance immune function in cyclophosphamide-induced immunosuppressed mice via gut microbiota modulation and metabolic pathway regulation.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {190}, number = {}, pages = {118387}, doi = {10.1016/j.biopha.2025.118387}, pmid = {40749338}, issn = {1950-6007}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Cyclophosphamide ; *Bacillus/chemistry ; *Polysaccharides/pharmacology/isolation & purification ; Mice ; *Metabolic Networks and Pathways/drug effects ; Male ; Cytokines/metabolism ; Mice, Inbred BALB C ; Colon/drug effects/pathology/immunology ; Immunosuppressive Agents ; *Immunocompromised Host/drug effects ; }, abstract = {In this study, we investigated the immunomodulatory effects of Bacillus velezensis GV1 polysaccharides (BPS) on gut microbial regulation in a cyclophosphamide (CTX)-induced immunosuppressed mouse model. BPS treatment significantly restored immune function, as evidenced by improvements in spleen and thymus indices and increased cytokine expression levels, including IL-6, TNF-α, IFN-γ, and IL-2. Additionally, BPS administration effectively alleviated the CTX-induced histopathological damage to the colon, enhanced tissue repair, and maintained epithelial integrity. The beneficial effects of BPS were associated with the selective modulation of the gut microbiota, and notably enhanced beneficial bacterial taxa, including PAC001112_g, PAC001074_g (Muribaculaceae), Monoglobus, PAC001500_g (Peptococcaceae), and PAC002153_g (Lachnospiraceae). Metagenomic analysis further revealed key metabolic pathways affected by BPS, such as folate biosynthesis, fructose and mannose metabolism, and pentose and glucuronate interconversion, involving essential enzymes such as xylulokinase, triosephosphate isomerase (TIM), and fructan beta-fructosidase. Collectively, these findings indicate that BPS effectively alleviates CTX-induced immunosuppression by modulating gut microbiota composition, underscoring its potential as a valuable supplementary or functional agent with immune-enhancing effects.}, } @article {pmid40728316, year = {2025}, author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR}, title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40728316}, issn = {1751-7370}, support = {2018-07819//USDA NIFA Postdoctoral Fellowship/ ; //Rice University Department of BioSciences/ ; CSP-503794//US Department of Energy Joint Genome Institute Community Science Program/ ; }, mesh = {*Symbiosis ; *Microbiota ; *Genome, Bacterial ; *Cyanobacteria/genetics/physiology ; Metagenome ; Phylogeny ; Nitrogen Fixation ; *Ferns/microbiology ; Plant Leaves/microbiology ; }, abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet, the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.}, } @article {pmid40695175, year = {2025}, author = {Federico, S and Esposito, R and De Rosa, M and Sonnessa, M and Reddel, S and Laurenzi, G and Bertolino, M and Giovine, M and Pozzolini, M and Zupo, V and Costantini, M}, title = {Comparative metagenomic analyses of the microbiome from three Mediterranean sponges to identify genes involved in biosynthesis of bioactive compounds.}, journal = {Marine genomics}, volume = {82}, number = {}, pages = {101202}, doi = {10.1016/j.margen.2025.101202}, pmid = {40695175}, issn = {1876-7478}, mesh = {Animals ; *Porifera/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; }, abstract = {Marine sponges host a range of microorganisms and among them, bacteria represent a significant part of their biomass. Furthermore, bacteria are promising sources of natural products to be applied in various fields. Often the study their biotechnological potential is relented by low grow rates. For this reason, such cultivation-independent approaches, as metagenomics tools applied to sponges is obtaining wide success. For the first time, here we aimed at having an almost complete information about taxonomic and functional diversity of bacteria associated to three sponges, Agelas oroides, Haliclona (Halichoclona) vansoesti and Geodia cydonium, previously reported as candidate sources of bioactive compounds for pharmacological, nutraceutical and cosmeceutical purposes. Comparative metagenomic analyses were applied, sequencing DNA from the three sponges by ONT GridION X5 Mk1 sequencer. Our findings revealed for all the analyzed sponges the presence of genes/enzymes responsible for the synthesis of vitamins, fatty acids, antioxidant glutathione, terpenes, steroids and carotenoids. Consequently, we demonstrated the three sponges under analysis and their associated microorganisms could be considered good candidates for the isolation and identification of bioactive compounds for biotechnological application in the field of pharmacology, nutraceuticals and cosmeceuticals as well as environmental biotechnologies. Overall, metagenomic data represent a useful tool exploitable to sustainably develop bioactive products.}, } @article {pmid40633493, year = {2025}, author = {Sibinga, NA and Werner, E and Tegtmeier, D and De Smet, J}, title = {Animal board invited review: The need for, and the path towards, a functional understanding of the farmed insect microbiome.}, journal = {Animal : an international journal of animal bioscience}, volume = {19}, number = {8}, pages = {101575}, doi = {10.1016/j.animal.2025.101575}, pmid = {40633493}, issn = {1751-732X}, mesh = {Animals ; *Tenebrio/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; *Diptera/microbiology ; *Animal Husbandry ; }, abstract = {The rapid growth of research on industrially produced insect species over the past two decades has coincided with breakthroughs in the speed and affordability of DNA sequencing. This has allowed researchers to rapidly generate data on the microbial communities associated with farmed insects, especially the gut-residing bacteria of the two cornerstone production species: black soldier fly (BSF, Hermetia illucens) and yellow mealworm (Tenebrio molitor). A picture of the most prevalent and abundant microbes associated with these species has rapidly come into focus. Specific microbial functions have been suggested under extreme or challenging rearing settings, but less is known about the contributions of the microbiome to insect rearing under realistic production conditions. There is limited understanding of how microbial communities of farmed insects arise, are maintained, and change in response to stimuli. Likewise for seemingly basic questions: what functions do insect-associated microbes perform for the host? Which (if any) taxa are essential for healthy insects? This is not intended as a criticism of existing research; indeed, these questions turn out not to be simple. Answering them requires targeted research approaches testing specific hypotheses about farmed insect microbiome function. This review aims to recalibrate the state of knowledge by critically assessing common and emerging strategies to study these microbiomes and existing knowledge gaps about the functional role of the microbiome for BSF and mealworm. Overall, it is clear that microbes are an intrinsic part of the ecology of these two farmed insects. Reciprocal interactions between microbes and insects are extensive, though microbiome community composition depends to a large extent on environmental conditions. To date, it remains unclear how taxonomical shifts correspond to functional shifts and to what extent such changes impact insect physiology. For example, when mealworms are fed plastics, their microbiomes undergo significant changes in microbial composition. These changes are presumed to increase the ability of mealworms and their microbiota to degrade plastic, but this change in function is hard to conclusively demonstrate with current tools. Furthermore, analysis of the literature shows that taxonomically disparate microbial communities may provide similar functional benefits, e.g. lignocellulose breakdown in BSF larvae. This review therefore aims to critically assess the state of the art with regard to functional analysis of the farmed insect microbiome and how available experimental methods can be best applied to identify links between microbial functions and insect physiology and improve the efficiency and sustainability of the farmed insect industry.}, } @article {pmid40484397, year = {2025}, author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y}, title = {Field dynamics of the root endosphere microbiome assembly in paddy rice cultivated under no fertilizer input.}, journal = {Plant & cell physiology}, volume = {66}, number = {7}, pages = {1086-1101}, doi = {10.1093/pcp/pcaf045}, pmid = {40484397}, issn = {1471-9053}, support = {18H02467//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; 24K21870//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; JPMJTR23UJ//Japan Science and Technology Agency/ ; JPMJSP2140//JST SPRING, Japan/ ; }, mesh = {*Oryza/microbiology/growth & development ; *Plant Roots/microbiology ; *Microbiota/genetics ; Fertilizers ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Metagenome ; Nitrogen Fixation ; Bacteria/genetics ; }, abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared with a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.}, } @article {pmid40439988, year = {2025}, author = {Davidson, IM and Nikbakht, E and Haupt, LM and Dunn, PJ}, title = {Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.}, journal = {Journal of assisted reproduction and genetics}, volume = {42}, number = {7}, pages = {2421-2436}, pmid = {40439988}, issn = {1573-7330}, mesh = {Female ; Humans ; *Vagina/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Computational Biology/methods ; Adult ; Chlamydia trachomatis/genetics/isolation & purification/pathogenicity ; Australia ; Reproductive Techniques, Assisted ; }, abstract = {PURPOSE: Rising demand for assisted reproductive technologies (ART) with limited improvements in success rates has driven interest in the impact of the vaginal microbiome on fertility outcomes. In order to fully examine the relationship between the vaginal microbiome and fertility outcomes, methodologies and technological developments must be standardised and benchmarked to provide the most accurate assessment of microbial population representation.

METHODS: This study sought to investigate the utility of 16S sequencing and bioinformatic approaches using nanopore sequencing to characterize core vaginal microbiota in a healthy Australian cohort of reproductive-age women.

RESULTS: Optimisation and comparison of different PCR strategies for whole 16S amplification was undertaken, along with the generation of bioinformatic analysis strategies. Initial qPCR identified the 27F-YM (MIX) primer as the most sensitive for C. trachomatis. However, nanopore sequencing revealed no detectable C. trachomatis across all six samples. Among the bioinformatic tools, Porechop with NanoCLUST most accurately identified microbial presence. Community state type (CST) I-characterised by Lactobacillus crispatus dominance-was identified as the most common CST (66%), aligning with patterns of a healthy vaginal microbiome.

CONCLUSION: The findings highlight a Lactobacillus-rich microbiome as the most common among healthy females; however, further refinement-potentially through a metagenomics approach-is recommended to address 16S rRNA primer limitations to enable improved accuracy of microbial detection for the vaginal microbiome.}, } @article {pmid40437943, year = {2025}, author = {Franzin, M and Lagatolla, C and Forgiarini, SS and Haag, M and Neef, SK and Comar, M and Schaeffeler, E and Bellich, B and Bramuzzo, M and Decorti, G and Lucafò, M and Hofmann, U and Schwab, M and Stocco, G}, title = {Klebsiella pneumoniae contributes to altered cytotoxicity of thiopurines in vitro: Possible implications of biotransformation and bacterial metabolism.}, journal = {British journal of pharmacology}, volume = {182}, number = {18}, pages = {4281-4298}, doi = {10.1111/bph.70089}, pmid = {40437943}, issn = {1476-5381}, support = {RC 07/22//Italian Ministry of Health, through the contribution given to the Institute for Maternal and Child Health IRCCS Burlo Garofolo/ ; //Robert Bosch Stiftung/ ; }, mesh = {Humans ; *Klebsiella pneumoniae/metabolism ; Biotransformation ; Jurkat Cells ; Inflammatory Bowel Diseases/drug therapy/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome ; *Mercaptopurine/metabolism/pharmacology ; Cell Survival/drug effects ; Child ; }, abstract = {BACKGROUND AND PURPOSE: Thiopurines are used in paediatric inflammatory bowel disease (IBD), but some patients do not respond. Because the gut microbiota influences drug efficacy and IBD-patient microbiota presents increased bacterial abundance, we investigated the impact of candidate Enterobacteriaceae on drug cytotoxicity, metabolism and efficacy.

EXPERIMENTAL APPROACH: Thiopurines were exposed in vitro to bacteria for 4 h at 37°C and drug concentrations measured by UV spectrophotometry. Cytotoxic effects and drug metabolite concentrations on NALM6 and JURKAT cells were determined after treatment with thiopurines exposed or not to bacteria. Drugs were measured in Klebsiella pneumoniae lysates and bacterial conditioned media were used for metabolomic analyses. Shotgun metagenomic sequencing was performed on eight IBD-patient faecal stools.

KEY RESULTS: Incubation of thiopurines with K. pneumoniae, but not Escherichia coli and Salmonella enterica, reduced thiopurine concentrations and cytotoxicity on NALM6 and JURKAT cells. Thiopurine metabolites were lower in cells treated with drugs previously exposed to K. pneumoniae. Internalisation of drugs was demonstrated by their detection in lysates after bacterial incubation. Untargeted metabolomics revealed biotransformation of thiopurines by K. pneumoniae, as reactions of deconjugation, reduction, glycosylation, acetylation or conjugation with propionic acid. Incubation with thiopurines led to changes in the secretion of endogenous bacterial metabolites. K. pneumoniae faecal abundance was associated with lower thiopurine metabolite concentrations in erythrocytes of paediatric IBD-patients.

CONCLUSIONS AND IMPLICATIONS: K. pneumoniae decreases the cytotoxicity of thiopurines through internalisation of MP and TG. We revealed potential bacterial drug biotransformation, as well as negative correlations between bacterial abundance and drug metabolites.}, } @article {pmid40118220, year = {2025}, author = {Rozera, T and Pasolli, E and Segata, N and Ianiro, G}, title = {Machine Learning and Artificial Intelligence in the Multi-Omics Approach to Gut Microbiota.}, journal = {Gastroenterology}, volume = {169}, number = {3}, pages = {487-501}, doi = {10.1053/j.gastro.2025.02.035}, pmid = {40118220}, issn = {1528-0012}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Metabolomics/methods ; *Metagenomics/methods ; *Proteomics/methods ; *Artificial Intelligence ; *Genomics/methods ; Multiomics ; }, abstract = {The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depiction of the gut microbial ecosystem's complexity. However, these tools generate a large data stream in which integration is needed to produce clinically useful readouts, but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools have potential for clinical implementation, including discovery of microbial biomarkers for disease classification or prediction, prediction of response to specific treatments, and fine-tuning of microbiome-modulating therapies. The state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome are discussed.}, } @article {pmid40851072, year = {2025}, author = {Zhang, L and Wang, S and Wong, MCS and Mok, CKP and Ching, JYL and Mak, JWY and Chen, C and Huo, B and Yan, S and Cheung, CP and Chiu, EOL and Fung, EYT and Cheong, PK and Chan, FKL and Ng, SC}, title = {The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {171}, pmid = {40851072}, issn = {2055-5008}, support = {COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; NCI202346//New Cornerstone Science Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Aged ; *Synbiotics/administration & dosage ; SARS-CoV-2/immunology ; Female ; Male ; *COVID-19/prevention & control/immunology ; *COVID-19 Vaccines/immunology/administration & dosage ; Feces/microbiology ; Bifidobacterium ; *Immunogenicity, Vaccine ; *Diabetes Mellitus/immunology/microbiology ; Vaccination ; BNT162 Vaccine/immunology ; Middle Aged ; Antibodies, Viral/blood ; }, abstract = {The study aims to tackle the seed and soil microbiome and mechanisms that contribute to the effect of synbiotics in enhancing immunogenicity after SARS-CoV-2 vaccination in elderly and diabetic patients. Among 369 subjects who received 3 months of SIM01, a gut microbiota-derived synbiotic formula of three Bifidobacterium strains (B. adolescentis, B. bididum, and B. longum) or a placebo after the SARS-CoV-2 vaccines (mRNA vaccine BNT162b2 (Pfizer-BioNTech) or the inactivated vaccine Sinovac-CoronaVac), we performed metagenomic sequencing in stool samples of 280 vaccinees collected at baseline and 3-month postvaccination and metabonomic sequencing in 276 vaccinees collected at baseline and 1-month postvaccination. The open niche of autochthonous gut microbiota (lower levels of Bifidobacterium and decreased functional potential for carbohydrate metabolism) was associated with enhancing SIM01-contained species. The enrichment of three bifidobacterial species after 3 months of SIM01 intervention (BABBBL_fc) was positively correlated with the level of neutralizing antibodies to the BNT162b2 vaccine at 6-month postvaccination. The fold change of benzoic acid was positively correlated with BABBBL_fc in the BNT162b2 vaccinees, which was also implicated with SARS-CoV-2 surrogate virus neutralization test (sVNT)% levels at 1-month postvaccination. Importantly, SIM01 strain engraftment assessed by StrainPhlAn (A metagenomic strain-level population genomics tool) was associated with a higher fold change of three bifidobacterial species and could be predicted based on the baseline gut microbiome. Therefore, the resident gut microbiome affected the SIM01 engraftment, which was associated with the immunogenicity of SARS-CoV-2 BNT162b2 vaccines.}, } @article {pmid40850953, year = {2025}, author = {Tang, M and Li, C and Ge, X and Kuang, Y and Qiu, L and Chan, KC and Chen, Z and Guo, L and Zhao, Z and Zhang, B and Liu, S and Zhou, X}, title = {Honeybee-Gilliamella synergy in carbohydrate metabolism enhances host thermogenesis in cold acclimation.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {172}, pmid = {40850953}, issn = {2055-5008}, support = {RDF-23-01-067//Research Development Fund of Xi'an Jiaotong-Liverpool University/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 32470455//National Natural Science Foundation of China/ ; 2023IOZ0104//program from Institute of Zoology, Chinese Academy of Sciences/ ; No.SYND-2021-30//Program from the Sanya Institute of China Agricultural University/ ; }, mesh = {Animals ; Bees/microbiology/physiology ; *Carbohydrate Metabolism ; Cold Temperature ; *Acclimatization ; *Thermogenesis ; Gastrointestinal Microbiome ; Glucose/metabolism ; Symbiosis ; Metagenomics ; Metabolomics ; Pyruvic Acid/metabolism ; }, abstract = {How gut symbionts contribute to host adaptation remains largely elusive. Studying co-diversified honeybees and gut bacteria across climates, we found cold-adapted species (Apis mellifera, A. cerana) exhibit enhanced genomic capacity for glucose, pyruvate, lipid and glucuronate production versus tropical species. Metagenomics revealed Gilliamella as the most enriched gut bacterium in cold-adapted bees. Germ-free honeybees inoculated with the Gilliamella from A. cerana showed increased activity, body temperature and fat storage upon cold exposure. Saccharide metabolomics demonstrated higher hindgut glucose levels in Gilliamella-colonized A. mellifera versus germ-free bees, and in A. cerana versus three sympatric tropical species. Although Gilliamella can hydrolyze β-glucan into glucose, cultural experiments suggest it preferentially degrades glucuronate to pyruvate. In turn, monocolonized bees upregulated hindgut glucose/pyruvate utilization while increasing glucuronate provision, suggesting nutritional complementarity. Gilliamella's transporter genes predominantly target ascorbate (a glucuronate derivative), which is elevated in inoculated hindguts. Accordingly, Gilliamella converts ascorbate to D-xylulose-5P (promoting lipogenesis), while showing reduced growth on glucuronate/ascorbate versus glucose, potentially minimizing glucose competition with hosts. We revealed a highly coordinated host-symbiont metabolic synergy enhancing host energy acquisition for cold adaptation.}, } @article {pmid40849632, year = {2025}, author = {Jang, S and Lee, EJ and Park, S and Lim, H and Ahn, B and Huh, Y and Koh, H and Park, YR}, title = {Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {189}, pmid = {40849632}, issn = {2049-2618}, mesh = {Humans ; *Crohn Disease/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Child ; Male ; *Bacteria/classification/genetics/isolation & purification ; Female ; *Ileum/microbiology/pathology ; Prospective Studies ; Adolescent ; Transcriptome ; Gene Expression Profiling ; Metagenome ; Computational Biology/methods ; *Host Microbial Interactions/genetics ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.

RESULTS: In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.

CONCLUSIONS: Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.}, } @article {pmid40683476, year = {2025}, author = {Díaz-Moreno, N and Lobos, C and Carvajal, A and Poblete, I and Cantera, S and Lebrero, R}, title = {Valorization of aromatic hydrocarbons into polyhydroxyalkanoates: advances towards sustainable waste gas treatment.}, journal = {Bioresource technology}, volume = {436}, number = {}, pages = {132991}, doi = {10.1016/j.biortech.2025.132991}, pmid = {40683476}, issn = {1873-2976}, mesh = {*Hydrocarbons, Aromatic/chemistry/metabolism ; *Polyhydroxyalkanoates/chemistry/metabolism ; *Waste Management ; *Bioreactors/microbiology ; Sustainable Development ; Gases/chemistry/metabolism ; Pseudonocardia/metabolism ; Rhodococcus/metabolism ; Microbial Consortia ; Nitrogen/metabolism ; *Biopolymers/biosynthesis ; }, abstract = {Benzene, toluene, ethylbenzene, xylene and styrene (BTEXS) are priority gaseous pollutants due to their widespread release and health risks. This study demonstrates an efficient BTEXS bioconversion process into polyhydroxyalkanoates (PHA) using a specialized mixed microbial culture dominated by Pseudonocardia and Rhodococcus. The consortium achieved simultaneous degradation rates of 15.1 ± 3.9 g m[-3]h[-1] for toluene and 17.6 ± 5.7 g m[-3]h[-1] for ethylbenzene, with removal efficiencies over 90 %. The operating strategy promoted PHA accumulation up to 21.4 % gPHA gDCW[-1]. A two-step process was successfully implemented consisting of an initial reactor for biomass growth followed by a second reactor under nitrogen deprivation. PHA analysis revealed the synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer with a dynamic increase in 3-hydroxyvalerate content under prolonged nitrogen starvation. Metagenomics provided insights into the microbial networks and metabolic pathways involved in the process. This research offers a sustainable solution for mitigating BTEXS pollution while producing valuable bioplastics.}, } @article {pmid40680679, year = {2025}, author = {Ni, H and Wang, J and Wu, H and Chan, BK and Chen, K and Wang, H and Chan, EW and Li, F and Chen, S}, title = {Exposure to the growth promoter tylosin elicits gut microbiota disruption and metabolic imbalance in mouse model.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109684}, doi = {10.1016/j.envint.2025.109684}, pmid = {40680679}, issn = {1873-6750}, mesh = {*Tylosin/toxicity/adverse effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Anti-Bacterial Agents/toxicity/adverse effects ; Mice, Inbred C57BL ; Male ; *Growth Substances/toxicity ; }, abstract = {The environmental risk associated with the usage of the antibiotic tylosin as an animal growth promoter (AGPs) needs to be assessed because such agents are used in abundance and contamination of the environment is common, yet their effects on the physiology and gut microbiota composition of animals and humans are poorly understood. In this work, we performed metagenomic analysis and revealed that tylosin significantly disrupted the gut microbiota structure of animals, reduced species diversity, and caused the increase in the relative abundance of Blautia (60.95%). Enrichment of multiple contigs containing ARGs was observed, indicating that tylosin promotes antimicrobial resistance (AMR) development. Transcriptomic analyses of ileum tissues revealed perturbation in gene expression patterns suggestive of mitochondrial dysfunction and energy metabolism imbalance. These alterations might compromise nutrient absorption and utilization in the GI tract, and heighten the risk of development of obesity and non-alcoholic fatty liver disease (NAFLD). Furthermore, downregulation of immune-related gene expression was observed, indicating that tylosin caused immunosuppression and increased susceptibility to microbial infections when used over extended periods. Integrated omics analysis of the liver also showed significant disturbances in metabolism through activation of the arachidonic acid metabolism pathway, exacerbating inflammatory responses, and precipitating the occurrence of metabolic disorders such as type 2 diabetes mellitus (T2DM) and NAFLD. Our findings unveil the detrimental effects of tylosin on animal gut microbiota and metabolic functions and highlight the potential health risks to wildlife and humans when released into the environment. These findings highlight a need for cautious use of AGPs and the development of safer alternatives.}, } @article {pmid40532535, year = {2025}, author = {Wang, Z and He, Y and Luo, M and Liu, S and Hou, J and Cao, B and An, X}, title = {Transfer toxicity of polystyrene microplastics in vivo: Multi-organ crosstalk.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109604}, doi = {10.1016/j.envint.2025.109604}, pmid = {40532535}, issn = {1873-6750}, mesh = {Animals ; *Microplastics/toxicity ; Mice ; *Polystyrenes/toxicity ; Female ; Gastrointestinal Microbiome/drug effects ; Liver/drug effects ; }, abstract = {The accumulation of microplastics (MPs) within the environment caused serious ecological and health problems. Nevertheless, its systemic toxicity to organisms and its mechanisms lack effective evidence. This study established a model of MP exposure through the gavage of polystyrene (PS)-MPs particles to maternal mice on days 1 to 21 of lactation. The results demonstrated that PS-MPs were distributed widely in maternal mice, occurring mainly in the feces, colon, liver and mammary glands. Further experiments revealed that the gut and blood-milk barriers were disrupted, and pathological injury and inflammatory reactions were observed in the liver, gut, and mammary glands. Metabolomic and metagenome analysis indicated abnormalities in hepatic bile acid metabolism and significant alterations in the gut microbiota after exposure to PS-MPs. These alterations led to increased disruption of the intestine-liver axis. Notably, with fecal microbiota transplantation and antibiotic experiments, we observed that elimination of the intestinal microbiota reduced tissue inflammation and improved gut and blood-milk barrier leakage. These findings demonstrated that PS-MPs exaggerated intestine-liver axis disorders by inducing colonic injury, intestinal ecological dysregulation and abnormal hepatic bile acid metabolism. Furthermore, PS-MPs translocated via the intestine-liver axis and exerted broader toxic effects on mammary tissue. Overall, our study uncovered the transfer toxicity of PS-MPs in mice, proposing the possibility of a gut-liver-mammary axis.}, } @article {pmid40527192, year = {2025}, author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG}, title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109611}, doi = {10.1016/j.envint.2025.109611}, pmid = {40527192}, issn = {1873-6750}, mesh = {*Sewage/microbiology ; *Microbiota/drug effects ; Textiles ; *Drug Resistance, Microbial/genetics ; *Microplastics/analysis ; Virulence Factors/genetics ; *Water Pollutants, Chemical/analysis ; }, abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.}, } @article {pmid40849482, year = {2025}, author = {Zhang, Y and Liao, YT and Liu, F and Li, RW and Wu, VCH}, title = {Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {190}, pmid = {40849482}, issn = {2049-2618}, support = {2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; }, mesh = {Animals ; Cattle ; *Virome/genetics ; Metagenomics/methods ; *Animal Feed/analysis ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; *Poaceae ; *Diet/veterinary ; *Edible Grain ; }, abstract = {BACKGROUND: In the United States beef industry, grain-feeding and grass-feeding are the two most common types of cattle feeding. Different feeding methods are likely to affect gut microbiota compositions and subsequently change microbial adaptation and cattle metabolism. However, there is limited information regarding the impact of diet on cattle gastrointestinal virome. This study examined the composition of fecal virome from grain-fed and grass-fed beef cattle and identified unique virome features to understand the relationship between these two feeding types.

RESULTS: Six grain-fed and six grass-fed Angus beef cattle were weighed, and their fecal samples were collected for further viral metagenomic sequencing. The difference in animal growth revealed a significantly higher post-weaning weight in grain-fed cattle than in grass-fed cattle after day 56. Furthermore, the analysis of the fecal viral population showed that approximately 795 and 1266 predicted viral sequences were obtained in the grain-fed and grass-fed samples, respectively. Among those, 54.3% of the grain-fed and 26.3% of the grass-fed viral sequences were identified as known viruses. The taxonomic classification showed that viruses belonging to the order Caudovirales, mostly bacteriophages, dominated the cattle virome in both sample groups, followed by the order Cremeviriles and Petitvirales. At the family level, 13 and 16 different viral families were detected in the grain and grass-fed groups, respectively. The comparison of virome features from the two groups indicated that the viral population from the kingdom Bamfordvirae had a significantly higher abundance in the grain-fed group than in the grass-fed cattle virome. In contrast, the kingdom Heunggongvirae had a significantly higher abundance in the grass-fed group than in the grain-fed cattle virome. Moreover, the viruses, belonging to the order Caudovirales and the family Podoviridae, had significantly higher abundances in the grass-fed virome than in the grain-fed virome.

CONCLUSIONS: The findings indicate the influence of animal feeds on the changes in gastrointestinal viral compositions and their potential association with cattle weight gain. The current outcome can contribute to further understanding of phage-bacterial interactions and their underlying mechanisms in regulating the animal host's metabolism and feed efficiency. Video Abstract.}, } @article {pmid40847279, year = {2025}, author = {Azmi, MAI and William-Dee, J and Morni, MA and Azhar, NAA and Sabarudin, NA and Jinggong, ER and Zolkapley, S and Baharom, NIM and Haqeem, MD and Sien, VL and Mohamad Azmi, AH and Adrus, M and Tan, CS and Khan, FAA}, title = {Metagenomic insights into host-specific gastroenteritis bacteria in forest rodents of Sarawak, Borneo: implications for one health surveillance of rodent-borne pathogens.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {531}, pmid = {40847279}, issn = {1471-2180}, support = {GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; F07/PGRG/2046/2020//Postgraduate Research Grant, UNIMAS/ ; }, mesh = {Animals ; *Gastroenteritis/microbiology/veterinary ; Borneo/epidemiology ; Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Forests ; *Rodentia/microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; One Health ; Host Specificity ; Phylogeny ; Zoonoses/microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; *Rodent Diseases/microbiology ; }, abstract = {Rodents are known to act as reservoirs for zoonotic diseases due to their widespread distribution and synanthropic nature. Among these, foodborne pathogens capable of causing gastroenteritis in humans are of particular concern, as rodents can facilitate their transmission through contamination of food sources. Forest-dwelling rodents may harbour bacterial taxa native to their habitat, posing a risk of zoonotic spillover to nearby human settlements. This risk is further heightened by the growing prevalence of ecotourism activities, particularly in tropical countries like Malaysia. In this study, rodent trapping was conducted in selected forested areas adjacent to human settlements across Sarawak. Nanopore sequencing of the full-length 16 S rRNA gene was conducted on faecal DNA from 46 rodent individuals representing seven different species (Maxomys surifer, M. tajuddinii, M. whiteheadi, Niviventer cremoriventer, Rattus tanezumi, R. tiomanicus and Sundamys muelleri). A total of ten bacterial species associated with gastroenteritis were successfully detected. Notable findings in this study include Campylobacter, Salmonella and Shigella species, which are known to cause bacterial gastroenteritis in humans. Also, the presence of certain bacterial taxa in specific rodent genera suggests potential host specificity of foodborne pathogens. This study highlights the potential public health risks caused by rodent-borne bacterial transmission and the importance of monitoring forest rodents as potential reservoirs of zoonotic pathogens.}, } @article {pmid40683452, year = {2025}, author = {Timilsina, M and Chundru, D and Pradhan, AK and Blaustein, RA and Ghanem, M}, title = {Benchmarking Metagenomic Pipelines for the Detection of Foodborne Pathogens in Simulated Microbial Communities.}, journal = {Journal of food protection}, volume = {88}, number = {9}, pages = {100583}, doi = {10.1016/j.jfp.2025.100583}, pmid = {40683452}, issn = {1944-9097}, mesh = {*Metagenomics/methods ; Food Microbiology ; Animals ; Benchmarking ; Listeria monocytogenes/isolation & purification ; Chickens ; Campylobacter jejuni/isolation & purification ; Cronobacter sakazakii/isolation & purification ; Food Contamination/analysis ; Microbiota ; }, abstract = {Foodborne pathogens pose a significant public health threat worldwide, despite modern advances in food safety. While molecular detection of pathogens in complex food matrices has gained attention to support tracking and preventing outbreaks, thorough benchmarking is needed to optimize workflows for specific scenarios. This study evaluated the performance of four metagenomic classification tools: Kraken2, Kraken2/Bracken, MetaPhlAn4, and Centrifuge, for estimating pathogen presence and abundance in simulated microbial communities representing three food products. Specifically, we evaluated workflow performance in predicting varying levels of Campylobacter jejuni, Cronobacter sakazakii, and Listeria monocytogenes in metagenomes of chicken meat, dried food, and milk products. Metagenomes were simulated to include the respective pathogen at defined relative abundance levels (0%-control, 0.01%, 0.1%, 1%, and 30%) within the respective food microbiome. Performance evaluations demonstrated that Kraken2/Bracken achieved the highest classification accuracy, with consistently higher F1-scores across all food metagenomes, whereas Centrifuge exhibited the weakest performance. MetaPhlAn4 also performed well, particularly in predicting C. sakazakii in dried food metagenomes, but was limited in detecting pathogens at the lowest abundance level (0.01%). Overall, Kraken2/Bracken and Kraken2 exhibited the broadest detection range, correctly identifying pathogen sequence reads down to the 0.01% level, whereas MetaPhlAn4 and Centrifuge had higher limits of detection. Our results highlight Kraken2/Bracken as an effective tool for pathogen detection, with MetaPhlAn4 serving as a valuable alternative depending on pathogen prevalence. These findings provide crucial insights for selecting metagenomic tools for applications in food safety and pathogen surveillance applications.}, } @article {pmid40543402, year = {2025}, author = {Aziz, T and Shabbir, MA and Sarwar, A and Khan, AA and Zhao, L and Yang, Z and Shami, A and Alwethaynani, MS and Al-Asmari, F and Alghamdi, AM and Al-Joufi, FA}, title = {Exploring the multifaceted probiotic potential of Lactiplantibacillus plantarum NMGL2, investigating its antimicrobial resistance profiles and bacteriocin production.}, journal = {Journal of microbiological methods}, volume = {236}, number = {}, pages = {107178}, doi = {10.1016/j.mimet.2025.107178}, pmid = {40543402}, issn = {1872-8359}, mesh = {*Probiotics/pharmacology ; *Bacteriocins/biosynthesis/genetics ; *Lactobacillus plantarum/genetics/metabolism/drug effects/classification ; Phylogeny ; Genome, Bacterial ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Metagenomics ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Lactiplantibacillus plantarum is widely recognized for its probiotic and antimicrobial properties, making it a valuable candidate for food and clinical applications. Genomic characterization provides deeper insight into its potential health benefits and safety profile.

AIM: This study aimed to sequence and analyze the genome of L. plantarum NMGL2 to evaluate its antimicrobial resistance, probiotic potential, and genetic suitability for biotechnological applications.

METHODS: The genomic DNA of L. plantarum NMGL2 was extracted and sequenced using Illumina technology. Genome assembly and annotation were performed, followed by gene prediction using Prokka and identification of antimicrobial resistance genes, virulence factors, and probiotic markers via BLAST. Metagenomic analysis of gut microbiota samples and phylogenetic analysis were conducted to assess strain relationships with other L. plantarum isolates.

RESULTS: The genome analysis revealed approximately 3000 protein-coding genes, including those encoding bile salt hydrolase, antimicrobial peptides, and antibiotic resistance determinants. Phylogenetic analysis showed that NMGL2 is closely related to other probiotic L. plantarum strains, supporting its probiotic characteristics and its potential role in combating pathogens.

CONCLUSION: L. plantarum NMGL2 demonstrates promising probiotic traits and carries genes that support its application in food safety and clinical contexts. Further, in vivo studies are needed to validate its health benefits and ensure safety, particularly in treating gastrointestinal disorders.}, } @article {pmid40433987, year = {2025}, author = {Zhou, Z and Yang, M and Fang, H and Zhang, B and Ma, Y and Li, Y and Liu, Y and Cheng, Z and Zhao, Y and Si, Z and Zhu, H and Chen, P}, title = {Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {31}, pages = {e14232}, doi = {10.1002/advs.202414232}, pmid = {40433987}, issn = {2198-3844}, support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//Lanzhou Municipal Science and Technology Program/ ; 2024-8-30//Lanzhou Municipal Science and Technology Program/ ; 2024-4-2//Lanzhou Municipal Science and Technology Program/ ; 20250260006//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260016//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260020//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; }, mesh = {*Fusobacterium nucleatum/genetics/pathogenicity ; *Colorectal Neoplasms/microbiology ; Animals ; Mice ; Humans ; *Fusobacterium Infections/microbiology ; *Gastrointestinal Microbiome ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; }, abstract = {Polymorphic microbiomes play important roles in colorectal cancer (CRC) occurrence and development. In particular, Fusobacterium nucleatum (F. nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial for treatment. Here, multiple metagenomic sequencing cohorts are combined with multiomics to analyze the microbiome and related functional alterations. Furthermore, local human metagenome and metabolomics are used to discover commensal consortia. A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing result shows that F. nucleatum is more abundant in both the feces and tumor tissues of CRC patients. It causes alterations through various pathways, including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile acid metabolism disorders. The designed SynCom contains seven species with low competition interrelationship. Furthermore, the SynCom successfully inhibits F. nucleatum growth in vitro and achieves colonization in vivo. Additionally, it promotes F. nucleatum decolonization, and enhances tryptophan metabolism and secondary bile acid conversion, leading to reduced lipid accumulation, decreased inflammatory reaction, and enhanced tumor inhibition effect. Overall, the bottom-up designed SynCom is a controllable and promising approach for treating F. nucleatum-positive CRC.}, } @article {pmid40846880, year = {2025}, author = {Kotrbová, L and Grabicová, K and Švecová, H and Staňová, AV and Petrlíková, M and Grabic, R and Kodešová, R and Chroňáková, A}, title = {The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {30950}, pmid = {40846880}, issn = {2045-2322}, support = {QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; 063/2023/P//Grantová agentura Jihočeské univerzity v Českých Budějovicích/ ; }, mesh = {*Rhizosphere ; *Phaseolus/microbiology/drug effects/growth & development ; *Clarithromycin/pharmacology/metabolism ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Wastewater/chemistry ; Phylogeny ; Microbiota/drug effects ; }, abstract = {With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.}, } @article {pmid40846855, year = {2025}, author = {Zhang, M and Wang, X and Yao, H and Shen, Y and Teng, Y and Garber, PA and Pan, H and Li, M}, title = {Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {169}, pmid = {40846855}, issn = {2055-5008}, support = {32330015, 31821001//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Diet ; *Colobinae/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; }, abstract = {The effects of seasonal fluctuations in food availability on gut microbiome composition, diversity, and function present significant challenges to animals with hard-to-digest diets. Here, we investigate seasonal variation the gut microbiome of wild golden snub-nosed monkeys (Rhinopithecus roxellana), a foregut fermenting primate, using metagenomics and metatranscriptomics data. We reconstructed 578 metagenome-assembled genomes (MAGs), 76.5% of which did not have exact matches in reference databases, highlighting the novelty of their gut microbiota. The gut microbiome of wild golden snub-nosed monkeys exhibited high diversity and enrichment in plant secondary compound metabolism during summer, while in winter it was enriched with enzymes that function in lichen polysaccharide degradation and Lachnospiraceae, which is important for energy balance. Captive monkeys on a consistent diet showed minimal seasonal variation in gut microbiome composition. Habitat changes also affected golden snub-nosed monkey microbiota community assembly and carbon cycling pathways. These findings underscore the gut microbiome's plasticity in meeting host dietary needs under varying environmental conditions.}, } @article {pmid40846661, year = {2025}, author = {Qin, Q and Zhu, Y and Yang, L and Guo, R and Song, L and Wang, D and Li, W}, title = {Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.}, journal = {Chinese medical journal}, volume = {}, number = {}, pages = {}, pmid = {40846661}, issn = {2542-5641}, abstract = {BACKGROUND: The profile and clinical significance of the oral microbiome in patients with non-obstructive hypertrophic cardiomyopathy (noHCM) and obstructive hypertrophic cardiomyopathy (oHCM) remain unexplored. The objective of this study was to evaluate the difference of oral microbiome between noHCM and oHCM patients.

METHODS: This cross-sectional study enrolled 18 noHCM patients and 26 oHCM patients from Fuwai Hospital, Chinese Academy of Medical Sciences between 2020 and 2021. Clinical and periodontal evaluations were conducted, and subgingival plaque samples were collected. Metagenomic sequencing and subsequent microbial composition and functional analyses were performed.

RESULTS: Compared to oHCM patients, those with noHCM had higher systolic blood pressure (138.1 ± 18.8 mmHg vs. 124.2 ± 13.8 mmHg, P = 0.007), a larger body circumference (neck circumference: 39.2 ± 4.0 cm vs. 35.1 ± 3.7 cm, P = 0.001; waist circumference: 99.7 ± 10.5 cm vs. 92.2 ± 10.8 cm, P = 0.027; hip circumference: 102.5 ± 5.6 cm vs. 97.5 ± 9.1 cm, P = 0.030), a greater left ventricular end-diastolic diameter (46.6 ± 4.9 mm vs. 43.1 ± 4.9 mm, P = 0.026), and a lower left ventricular ejection fraction (64.1 ± 5.7 % vs. 68.5 ± 7.8%, P = 0.048). While overall biodiversity and general microbial composition were similar between the noHCM and oHCM groups, ten taxa displayed significant differences at the genus and species levels, with Porphyromonas gingivalis showing the highest abundance and greater enrichment in noHCM (relative abundance: 7.79535 vs. 4.87697, P = 0.043). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified ten distinct pathways, with pathways related to energy and amino acid metabolism being enriched in oHCM patients, and those associated with genetic information processing less abundant in the oHCM group. Metabolic potential analysis revealed ten significantly altered metabolites primarily associated with amino sugar and nucleotide sugar metabolism, porphyrin metabolism, pentose and glucuronate interconversion, and lysine degradation.

CONCLUSIONS: The higher abundance of Porphyromonas gingivalis, which is known to impact cardiovascular health, in noHCM patients may partially account for clinical differences between the groups. Pathway enrichment and metabolic potential analyses suggest microbial functional shifts between noHCM and oHCM patients, potentially reflecting inherent metabolic changes in HCM.}, } @article {pmid40844735, year = {2025}, author = {Bhatt, P and Rajesh, P and Kukkar, D and Kim, KH}, title = {Metagenomic profiling of gut microbime: associating their role with the advancement of diabetic nephropathy.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {9}, pages = {135}, pmid = {40844735}, issn = {1572-9699}, support = {DST/WISE-PhD/LS/2023/73/G//Department of Science and Technology, Ministry of Science and Technology, India/ ; EMDR/SG/13/2023-0756//Indian Council of Medical Research/ ; 2021R1A3B1068304//Ministry of Science, ICT and Future Planning/ ; 2022R1A6C101A779//National Center for Inter-University Research Facilities, Seoul National University/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Diabetic Nephropathies/microbiology ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/complications ; Disease Progression ; }, abstract = {Emerging evidence suggests that alterations in the gut microbiome should play a critical role in the development and progression of type 2 diabetes and its complication such as diabetic nephropathy (DN). Nevertheless, a considerable gap remains in our understanding of the interconnection between DN pathogenesis and gut microbiota arrangement. In this context, this review highlights recent research on the connection between the intestinal microbiota and DN risk, with a particular focus on the role of microbial metabolites in disease development. It also highlights recent advancements in metagenomic analyses of gut microbial communities and their potential contribution to the progression of DN. Further, it describes the challenges associated with the metagenomics-based analysis of intestinal microbiota and the advancement of therapeutics for DN. An exploration of the surveyed literature reveals the lack of any definitive correlation between gut microbiota and DN transition, even when assessed in view of widespread geographical and ethnic diversity. Future research in this domain should be conducted to address various issues like increasing the number of participants, intake patient diversity, logistical difficulties, and racial disparities. A critical assessment of these parameters will help improve our understanding of the potential contribution of gut microbiota to the DN progression.}, } @article {pmid40841874, year = {2025}, author = {Dinçer, S and Ülger, Y and Delik, A}, title = {Mucosal microbiota signatures reveal diagnostic insights in chronic liver disease.}, journal = {BMC gastroenterology}, volume = {25}, number = {1}, pages = {607}, pmid = {40841874}, issn = {1471-230X}, support = {CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; *Intestinal Mucosa/microbiology/pathology ; Female ; Case-Control Studies ; Metagenomics ; *Colon/microbiology/pathology ; Adult ; *Liver Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S ; Aged ; Chronic Disease ; Biopsy ; High-Throughput Nucleotide Sequencing ; Principal Component Analysis ; }, abstract = {PURPOSE: Chronic liver disease (CLD) and complications of cirrhosis are responsible for the deaths of approximately two million people per year worldwide. Abnormal intestinal permeability in the intestinal-liver axis and development of intestinal dysbiosis increase disease progression contributing to chronic systemic inflammation in CLD patients. The intestinal microbiota acts as a bioreactor for autonomous metabolic and immunological functions in regulating the host's response to external stimuli in the intestinal microbiota. The study aimed to analyze the gut microbiota profile from colonic mucosal biopsy materials in CLD patients using a metagenomic application.

MATERIALS AND METHODS: CLD and control groups were formed based on predefined inclusion and exclusion criteria from the study. In the metagenomic study, colonic mucosal biopsy material was studied from a total of 40 individuals, 20 with CLD and 20 healthy controls. We analyzed gut microbiota by 16 S rRNA metagenomic next-generation sequencing (NGS) method from colonic mucosal biopsy samples in CLD and healthy individuals. Metagenomic results were analyzed by Principal Component Analysis (PCA).

RESULTS: Significant differences were observed between the CLD and control groups across multiple taxonomic levels. At the phylum level, Proteobacteria were significantly enriched in CLD patients, while Firmicutes predominated in controls. Class-level analysis showed increased Gammaproteobacteria in CLD, the former associated with inflammatory pathways. At the order level, Enterobacterales were significantly higher in CLD (OR: 1.89, p = 0.04), whereas Clostridiales were more abundant in controls. Family-level comparisons revealed elevated Enterobacteriaceae in CLD, while Ruminococcaceae and Veillonellaceae were relatively preserved in controls. At the genus level, Prevotella and Streptococcus were increased in controls. Alpha diversity indices (Shannon, Chao1) were significantly lower in the CLD group (p < 0.001), indicating reduced microbial richness. Beta diversity analysis (PCoA, Bray-Curtis) showed distinct clustering between groups, supporting compositional divergence. Integration of metagenomic findings with biochemical markers (e.g.

, GGT: OR 0.79, p = 0.03) further underscored group-specific microbial signatures.

CONCLUSION: We observed a significant compositional shift in the gut microbiota of patients with CLD. Notably, pro-inflammatory taxa were increased and a decrease in beneficial bacterial groups involved in maintaining microbial homeostasis. Diversity analyses indicated a reduction in microbial richness in the CLD group. These findings may aid in identifying CLD-specific microbial signatures. Furthermore, integrating metagenomic data with biochemical parameters may contribute to improved diagnostic strategies.}, } @article {pmid40695592, year = {2025}, author = {Welsch, EC and Barron, MR and Storage, KM and Kazen, AB and Aboulalazm, FA and Kirby, JR and Kindel, TL}, title = {Gut microbiome and bile acid changes after male rodent sleeve gastrectomy: what comes first?.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {329}, number = {3}, pages = {R410-R421}, doi = {10.1152/ajpregu.00297.2024}, pmid = {40695592}, issn = {1522-1490}, support = {R01HL158900//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HL072483//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; Clowes Career Development Award//American College of Surgeons (ACS)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Gastrectomy/methods ; Male ; Mice, Inbred C57BL ; *Liver/metabolism ; Mice ; Fecal Microbiota Transplantation ; }, abstract = {Understanding how a sleeve gastrectomy (SG) achieves metabolic improvement is challenging due to the complex relationship between the liver, bile acid (BA) pool, and gut microbiome. We hypothesized that SG alters the gut microbiome, which then increases the BA pool, leading to metabolic efficacy. We performed fecal material transfer (FMT) from SG or sham mice to surgically naïve mice with an intact microbiome. We evaluated the effect of surgery and FMT on BA-related liver enzymes, BA concentrations, and gut microbiome composition via 16S and metagenomic analysis. SG significantly deflected weight gain compared with sham surgery, 5 ± 2 g versus 10 ± 3 g, respectively (P = 0.004). SG significantly increased the BA pool and decreased liver transcription of slc10a1 (P = 0.04) and cyp8b1 (P = 0.03). Random forest analysis identified several features with significantly increased relative abundance in SG compared with sham mice, including Lactobacillus. Examination of metabolic profiles with metagenomic analysis revealed a BA salt hydrolase produced by the Ligilactobacillus species. FMT of SG stool to surgically naïve mice significantly decreased the BA pool compared with sham FMT (P = 0.034). Unlike SG surgery, we found no effect of SG or sham FMT on bile acid-related enzymes in the liver after 14 wk of treatment. Overall, we propose that the metabolic benefits of SG surgery are related to decreased liver transcription of cyp8b1 and slc10a1 with subsequent increases in the systemic and enterohepatic BA pool, including lithocholic acid. The gut microbiome adapts to the altered BA pool with associated increases in Ligilactobacillus and bile salt hydrolase production.NEW & NOTEWORTHY We propose that the metabolic benefits of sleeve gastrectomy are initiated by decreased liver transcription of cyp8b1 and slc10a1. A notable downstream effect includes changes in systemic bile acid composition and circulation, including increased LCA. An altered gut microbiome after surgery includes increases in Ligilactobacillus that was shown to express a bile salt hydrolase, which could be a contributor to the post-sleeve gastrectomy gut microbiome changes.}, } @article {pmid40404216, year = {2025}, author = {Thng, KX and Tiew, PY and Mac Aogáin, M and Narayana, JK and Jaggi, TK and Ivan, FX and Shuttleworth, M and Long, MB and Richardson, H and Lind, H and Alferes de Lima Headley, D and Robertson, K and Pollock, J and Goeminne, PC and Shteinberg, M and De Soyza, A and Aliberti, S and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Ringshausen, FC and Lorent, N and Dimakou, K and Shoemark, A and Chalmers, JD and Chotirmall, SH}, title = {Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study.}, journal = {The European respiratory journal}, volume = {66}, number = {2}, pages = {}, doi = {10.1183/13993003.00054-2025}, pmid = {40404216}, issn = {1399-3003}, mesh = {Humans ; *Bronchiectasis/microbiology ; Europe ; *Sputum/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Aged ; Microbiota ; Prospective Studies ; High-Throughput Nucleotide Sequencing ; Pseudomonas aeruginosa/genetics/isolation & purification ; Haemophilus influenzae/genetics/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Streptococcus pneumoniae/genetics/isolation & purification ; Adult ; }, abstract = {BACKGROUND: The European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) registry shows considerable variation in culturable microbes in sputum between different European countries. The additive role of next-generation metagenomic sequencing remains unexplored and the association with antimicrobial resistomes unknown.

METHODS: We used next-generation shotgun metagenomic sequencing to prospectively assess sputum from 349 individuals recruited into the EMBARC Bronchiectasis Research Involving Databases, Genomics and Endotyping (BRIDGE) study from three European regions: Northern and Western Europe, Southern Europe and the UK. Samples were included from eight European countries. Microbiome and resistome profiles were assessed in relation to clinical outcomes.

RESULTS: Next-generation metagenomic sequencing reproduced differences between countries in microbial profiles that were previously shown by culture in the EMBARC study. Metagenomics provided enhanced detection for some bronchiectasis pathogens, including Pseudomonas aeruginosa, Haemophilus influenzae and Streptococcus pneumoniae. Three metagenomic microbial clusters dominated by the genera Pseudomonas, Streptococcus and Haemophilus demonstrated pan-European but variable distribution. Diverse resistomes, linked to underlying microbiomes, were identified across Europe, with significantly higher diversity of resistance gene determinants in Southern Europe. Resistome composition significantly differed between regions, characterised by regionally contrasting multidrug-resistant profiles. The EMBARC-BRIDGE cohort validated established bronchiectasis resistotypes RT1 and RT2, which occur at varying frequency across regions. Despite geographic variation in microbiome and resistome profiles in bronchiectasis across Europe, analogous antimicrobial resistance gene profiles associated with the key bronchiectasis genera Pseudomonas, Streptococcus and Haemophilus, independent of country or region.

CONCLUSION: Sputum metagenomics confirms and extends prior observations of regional variation in bronchiectasis microbiology. Important variation in the distribution of pathogens and antimicrobial resistance genes has implications for antimicrobial practices across Europe.}, } @article {pmid40153196, year = {2025}, author = {Erickson, I and Davidson, S and Choi, H and Rho, S and Guignet, M and Peagler, K and Thummel, K and Ericsson, A and Barker-Haliski, M}, title = {Intestinal dysbiosis alters acute seizure burden and antiseizure medicine activity in Theiler's virus model of encephalitis.}, journal = {Epilepsia}, volume = {66}, number = {8}, pages = {3022-3034}, doi = {10.1111/epi.18395}, pmid = {40153196}, issn = {1528-1167}, support = {//University of Washington/ ; }, mesh = {Animals ; *Dysbiosis/chemically induced/complications ; *Seizures/drug therapy/etiology/virology ; Male ; Mice ; Mice, Inbred C57BL ; *Theilovirus ; *Anticonvulsants/therapeutic use/pharmacokinetics/pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; *Carbamazepine/therapeutic use/pharmacokinetics/pharmacology/blood ; *Cardiovirus Infections/complications/drug therapy ; *Encephalitis/drug therapy/complications ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVE: Brain infection with Theiler's murine encephalomyelitis virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.

METHODS: Male C57BL/6J mice (4-5 weeks old) received oral ABX or saline (SAL) once daily beginning on arrival through day 7 after TMEV infection (postinfection [p.i.]). Mice were infected with TMEV or phosphate-buffered saline on day 0. Mice received intraperitoneal (20 mg/kg) CBZ or vehicle (VEH) twice daily on days 3-7 p.i. and were assessed for handling-induced seizures 30 min after treatment. Plasma was collected on day 7 p.i. at 15 and 60 min after CBZ administration for bioanalysis.

RESULTS: TMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX-CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment × ASM interaction (p = .0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p = .004). CBZ significantly increased latency to seizure presentation, an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.

SIGNIFICANCE: ABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV-induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an underrecognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.}, } @article {pmid40841555, year = {2025}, author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J}, title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7806}, pmid = {40841555}, issn = {2041-1723}, support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; }, abstract = {Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.}, } @article {pmid40841038, year = {2025}, author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X}, title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.}, journal = {Journal of environmental sciences (China)}, volume = {158}, number = {}, pages = {610-620}, doi = {10.1016/j.jes.2025.02.028}, pmid = {40841038}, issn = {1001-0742}, mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; }, abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.}, } @article {pmid40841030, year = {2025}, author = {Nie, E and He, P and Zhang, H and Lü, F}, title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.}, journal = {Journal of environmental sciences (China)}, volume = {158}, number = {}, pages = {516-526}, doi = {10.1016/j.jes.2024.10.007}, pmid = {40841030}, issn = {1001-0742}, mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; }, abstract = {Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.}, } @article {pmid40838847, year = {2025}, author = {Gao, X and Zheng, Y and Chang, H and Liu, J and Sun, X and Ren, Y and Li, L and Zhao, G and Cheng, Y and Ma, S and Zhao, J and Deng, J and Kang, T and Qiao, Z and Zhao, H and Xie, D and Wang, T and Li, S and Shi, H and Shi, A and Zhang, P}, title = {Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.}, journal = {Journal of medical virology}, volume = {97}, number = {8}, pages = {e70570}, doi = {10.1002/jmv.70570}, pmid = {40838847}, issn = {1096-9071}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Humans ; *Virome ; *Arthritis, Rheumatoid/diagnosis/virology ; *Metagenomics ; Male ; Female ; Middle Aged ; *Palatine Tonsil/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; Aged ; Microbiota ; }, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.}, } @article {pmid40836310, year = {2025}, author = {Wang, X and Dong, Q and Huang, P and Yang, S and Gao, M and Zhang, C and Zhang, C and Deng, Y and Huang, Z and Ma, B and Jiao, Y and Zhou, Y and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and Consortium, C and Tang, L and Hu, S and Duan, Y and Sun, W and Chen, W and Zhai, Q and Kong, X and Chen, L}, title = {The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {188}, pmid = {40836310}, issn = {2049-2618}, support = {32270077//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Genome, Viral ; Feces/virology/microbiology ; *Genetic Variation ; *Polymorphism, Single Nucleotide ; *Viruses/genetics/classification/isolation & purification ; China ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities.

RESULTS: Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.}, } @article {pmid40801952, year = {2025}, author = {Eckl-Dorna, J and Pjevac, P}, title = {[Principles of microbiome research].}, journal = {HNO}, volume = {73}, number = {9}, pages = {605-609}, pmid = {40801952}, issn = {1433-0458}, mesh = {*Microbiota/genetics ; Humans ; *Metagenomics/methods ; }, abstract = {Microbiome research in the ear nose and throat (ENT) field has substantially gained in importance in recent decades. Modern sequencing methods have largely replaced traditional cultivation. Standardized protocols are essential to ensure reliable and comparable data. The article explains key terms, such as microbiome (the entire microbial community and its environment) and microbiota (only living microorganisms), along with the microbial taxonomy. Important measures for microbiome assessment include the alpha-diversity (species richness and distribution within a sample) and beta-diversity (differences between samples). A differentiation is made between two main approaches to microbiome sequencing: 1) 16S rRNA gene amplicon sequencing (identifies microbial community composition by sequencing the PCR product of a specific gene), 2) metagenomic sequencing (sequences the entire genomic material of a sample, allowing deeper insights). As nasal microbiome biomass is low, careful study design and controls are crucial. Microbiome research is a rapidly growing field with great potential but it requires meticulous planning and bioinformatics expertise for meaningful results.}, } @article {pmid40674970, year = {2025}, author = {Göçer, S and Arı, O and Göçer, C and Durmaz, R}, title = {Metagenomic analysis of the middle ear microbiome: A next-generation sequencing approach in pediatric patients with and without effusion.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {196}, number = {}, pages = {112487}, doi = {10.1016/j.ijporl.2025.112487}, pmid = {40674970}, issn = {1872-8464}, mesh = {Humans ; Male ; Female ; Child ; Child, Preschool ; *Microbiota/genetics ; *Ear, Middle/microbiology ; *Metagenomics/methods ; *Otitis Media with Effusion/microbiology ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; }, abstract = {OBJECTIVES: Otitis media with effusion (OME) is one of the most common causes of reversible hearing loss in childhood. In recent years, host-microbiota interactions and alterations in microbiota composition associated with health and disease have gained increasing attention in the context of OME. This study aimed to investigate the bacterial microbiota composition of middle ear cavity (MEC) samples obtained from pediatric patients with and without OME. Microbiome differences were analyzed according to clinical groups and variables such as age and gender.

METHODS: 16S rRNA-based metagenomic sequencing was performed on MEC samples (n = 80) and nasopharyngeal samples (n = 20) obtained from 80 children-40 diagnosed with bilateral or unilateral OME (OME group) and 40 undergoing cochlear implant surgery without any history of otitis media (control group). The study cohort included 37 males and 43 females, aged between 2 and 11 years (mean age: 5.2 years).

RESULTS: Sequencing analysis revealed that the phyla Firmicutes and Proteobacteria were dominant in MEC samples. In the OME group, Firmicutes were significantly more abundant, whereas Proteobacteria levels were reduced. At the genus level, Alloiococcus was significantly enriched in the OME group, while genera considered potentially protective, such as Lactobacillus and Propionibacterium, were significantly decreased. Age was not significantly associated with microbial richness or evenness, suggesting stability of microbiota composition across age groups. However, a significantly higher relative abundance of Ralstonia was observed in female patients, suggesting that gender-related hormonal or immunological differences may influence the middle ear microbiota.

CONCLUSION: This study identifies a distinct microbiota profile associated with OME and suggests that host factors, particularly gender, may contribute to shaping the microbial and immunological landscape of the middle ear. These findings also indicate that the microbial environment in OME may shift toward a low-diversity, pathobiont-dominant state.}, } @article {pmid40626910, year = {2025}, author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S}, title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40626910}, issn = {1751-7370}, support = {//Shurl and Kay Curci Foundation/ ; GBMF9321//Gordon and Betty Moore Foundation/ ; }, mesh = {*Cyanobacteria/genetics/classification/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Fresh Water/microbiology ; Plasmids/genetics ; Metagenome ; }, abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by coculturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.}, } @article {pmid40833800, year = {2025}, author = {Kaspersen, HP and Estensmo, EL and Slettemeås, JS and Haverkamp, THA and Sjurseth, SK and Granstad, S and Sekse, C and Frederiksen, RF and Urdahl, AM}, title = {Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.}, journal = {Microbial genomics}, volume = {11}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001466}, pmid = {40833800}, issn = {2057-5858}, mesh = {Animals ; *Monensin/pharmacology ; *Turkeys/microbiology ; *Bifidobacterium/drug effects/genetics/classification/isolation & purification ; Poultry Diseases/prevention & control/microbiology ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Norway ; Female ; Male ; Coccidiosis/veterinary/prevention & control ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; *Coccidiostats/pharmacology ; }, abstract = {Intestinal tissue damage caused by coccidiosis is an important predisposing factor for necrotic enteritis in turkeys, and both diseases are common health issues in turkey production. In Norway, the in-feed ionophore coccidiostat monensin has been used as a preventive measure to combat coccidiosis since the late 1980s. In 2022, however, preventive use of monensin was phased out, which led to an undesired increase in antibiotic treatments among turkey flocks, largely due to necrotic enteritis. The aim of this study was to investigate the overall effects of the preventive monensin use and antibiotic treatment on the turkey caecal microbiota. A total of 102 flock samples from the Norwegian turkey population were included, and metagenomic datasets were generated through shotgun sequencing. All datasets were processed with the Taxprofiler pipeline, followed by diversity, redundancy and differential abundance analyses in R. A significant decrease in alpha and beta diversity was observed for the caecal samples from turkeys exposed to monensin, compared with the non-exposed. An increased abundance of Bifidobacterium spp. was observed in the samples from monensin-exposed turkeys, including Bifidobacterium pullorum, Bifidobacterium longum, Bifidobacterium pseudolongum, Bifidobacterium pseudocatenulatum and Bifidobacterium animalis. Additionally, a decrease in Megamonas and Megasphaera species was detected in these samples. Further, species within the Clostridium genus were higher in abundance among the samples from female turkeys compared with male turkeys. The results indicate that the use of monensin seems to decrease the overall diversity and promote the abundance of Bifidobacterium spp. in the caecum of turkeys, while decreasing the abundance of Megamonas and Megasphaera species. The use of monensin may be beneficial for the gut microbiota due to an increase in favourable Bifidobacterium spp. In contrast, treatment with phenoxymethylpenicillin (penicillin V) early in the turkey life cycle does not seem to cause long-term changes in the caecal microbiota composition. However, further studies are needed to investigate the effects of a decreased abundance of Bifidobacterium spp. and increased gut microbiota diversity in turkeys in the absence of monensin use.}, } @article {pmid40833454, year = {2025}, author = {Fong, GY and Chan, KG and Goh, WL and Yap, ML}, title = {Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {9}, pages = {134}, pmid = {40833454}, issn = {1572-9699}, support = {IPSR/RMC/UTARRF/2022-C1/Y01//Universiti Tunku Abdul Rahman/ ; }, mesh = {Animals ; *Columbidae/microbiology/virology ; *Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Metagenomics ; Viruses/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification/drug effects ; Metagenome ; Malaysia ; *Microbiota ; Biodiversity ; Phylogeny ; *Drug Resistance, Microbial/genetics ; }, abstract = {Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.}, } @article {pmid40832979, year = {2025}, author = {Zhou, W and Fan, Y and Zhang, X and Liu, M and Jiang, S and Shang, E and Duan, J}, title = {Amelioration of Guishao Yigong Decoction on Colorectal Cancer Through the Integration of 16S rRNA Sequencing and Fecal Metabolomics.}, journal = {Biomedical chromatography : BMC}, volume = {39}, number = {10}, pages = {e70198}, doi = {10.1002/bmc.70198}, pmid = {40832979}, issn = {1099-0801}, support = {ZDXM-3-9//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; }, mesh = {Animals ; *Colorectal Neoplasms/metabolism/drug therapy/microbiology ; *Feces/chemistry/microbiology ; *Drugs, Chinese Herbal/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; Mice ; Metabolomics/methods ; *Metabolome/drug effects ; Male ; }, abstract = {Guishao Yigong Decoction (GYD), a classical formula, has been used to treat colorectal cancer (CRC) in clinical practices. However, its mechanism is still unclear. Increasing evidence suggests that the gut microbiota may serve as a potential target for treating CRC. Therefore, this study aims to elucidate the amelioration and potential mechanism of GYD on CRC by comprehensively analyzing the metagenome of gut microbiota and fecal metabolome. The results indicated that GYD significantly reduced the number and size of adenomas in the mouse colon, decreased spleen index, alleviated mouse emaciation and rectal bleeding, and protected the colonic barrier. 16S rRNA gene sequencing analysis revealed that GYD could markedly improve the dysbiosis of gut microbiota in CRC mice, increasing the abundance of beneficial bacteria and decreasing the abundance of pathogenic bacteria. Furthermore, the disordered fecal metabolic profiling of CRC mice was notably reversed by GYD. Following GYD administration, metabolites such as thiamine pyrophosphate, 3-methylpentanoic acid, and propanoic acid significantly increased, whereas 2-hydroxy-2-methylpropanoic acid, levodopa, and stearic acid remarkably decreased. Correlation analysis further indicated a close relationship between differential gut microbiota and metabolites. In conclusion, the amelioration of GYD on CRC might involve the regulation of gut microbiota and its metabolism.}, } @article {pmid40832781, year = {2025}, author = {Tian, Y and Xu, Q and Wu, Z and Wang, H and Hu, X and He, N and Li, H and Liu, B and Zhong, Y and Zhang, H and Wang, M and Xiao, L and Li, S and Zou, Y}, title = {Ameliorating Effect of Bifidobacterium breve CM02-09T on High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease in Mice.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {16}, pages = {e70957}, doi = {10.1096/fj.202501250RR}, pmid = {40832781}, issn = {1530-6860}, support = {32100009//National Natural Science Foundation of China-Guangdong Joint Fund/ ; }, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy ; *Diet, High-Fat/adverse effects ; Male ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Mice ; *Bifidobacterium breve/physiology ; *Gastrointestinal Microbiome ; Liver/metabolism/pathology ; }, abstract = {Evidences have demonstrated that the regulation of gut microbiota by probiotics can be utilized to prevent nonalcoholic fatty liver disease (NAFLD); Bifidobacterium was widely used as a potential therapeutic alternative for metabolic diseases. In this study, the probiotic functions of Bifidobacterium breve CM02-09T and its effects on NAFLD were investigated through genome annotation and high-fat diet (HFD)-induced mouse model. The genome of B. breve CM02-09T consists of a single circular chromosome of 2 372 890 bp. Eighteen male C57BL/6J mice were fed a normal chow diet (NCD), a high-fat diet, and a high-fat diet (HFD) with B. breve CM02-09T separately for 12 weeks. Histopathology, lipid content, biochemical markers in the liver and blood, and metagenomics were assessed and compared. Our results indicate that supplementation with B. breve CM02-09T alleviated liver damage, reduced fat accumulation in the liver and epididymal adipose tissue, decreased TNF-α concentration, and improved NAFLD activity scores. Metagenomic analysis revealed that administration of B. breve CM02-09T promoted a decreased Firmicutes/Bacteroidetes ratio (F/B), an increase in beneficial bacteria, and enhanced lipid metabolism functions. Correlation analysis between the differential species and NAFLD-related indicators suggested that the anti-NAFLD effect of B. breve CM02-09T is related to the gut microbiota. Therefore, B. breve CM02-09T attenuates NAFLD by modulating the gut microbiota and could be used as an alternative therapeutic strategy.}, } @article {pmid40795028, year = {2025}, author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf078}, pmid = {40795028}, issn = {1574-6968}, support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; }, mesh = {Animals ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Humans ; Republic of Korea ; *Diptera/microbiology ; Phylogeny ; DNA, Bacterial/genetics ; Metagenomics ; }, abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.}, } @article {pmid40785530, year = {2025}, author = {Liang, J and He, J and Zhao, J and Yang, Y and Xu, W}, title = {Decline in the Relative Abundance of Antibiotic Resistance Genes in Long-Term Fertilized Soil and Its Driving Factors.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {33}, pages = {20710-20718}, doi = {10.1021/acs.jafc.5c03478}, pmid = {40785530}, issn = {1520-5118}, mesh = {Soil Microbiology ; *Fertilizers/analysis ; *Bacteria/genetics/drug effects/isolation & purification/classification/metabolism ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacterial Proteins/genetics/metabolism ; Microbiota ; Metals, Heavy/analysis ; }, abstract = {The changes in antibiotic resistance genes (ARGs) in long-term fertilized soil remain controversial. We aimed to analyze the variation characteristics of ARGs in long-term fertilized soil using metagenomic sequencing. The relative abundance of ARGs did not increase significantly after 7 years of fertilization. However, a clear decline in the relative abundance of ARGs was observed compared to the data from the 4th year. Microbial adaptation strategies in response to changes in the ARG abundance were associated with shifts in microbiome composition and function. Among these, bacterial abundance was the primary driving factor. Additionally, total heavy metal content might serve as the most significant co-selective pressure influencing ARG number. We believe that increasing the selective pressure from heavy metals and antibiotics might result in the loss of certain microbial species and a decrease in ARG abundance. This study provides novel insights into the variations of soil resistance genes under long-term fertilization.}, } @article {pmid40662747, year = {2025}, author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A}, title = {Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {8}, pages = {e0212424}, doi = {10.1128/aem.02124-24}, pmid = {40662747}, issn = {1098-5336}, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Soil/chemistry ; Cities ; Arizona ; *Viruses/genetics/classification/isolation & purification ; Desert Climate ; }, abstract = {Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.IMPORTANCEUrban green spaces are critical for the sustainability of arid cities. Nevertheless, they require deep soil physicochemical transformations. Soil bacterial and viral communities are responsible for soil functioning and provision of some ecosystem services, but they are also highly influenced by changes in the soil environment. The significance of our research is in illustrating the structural and functional changes that microbial and viral communities undergo in urban soils of arid cities and their potential impacts on urban greenspace soil processes.}, } @article {pmid40478395, year = {2025}, author = {Zhang, T and Liu, Y and Li, J and Yuan, M and Qiao, C and Huang, X and Yang, X and Gao, B and Lou, C and Yang, Y and Cao, Y}, title = {Toad's survivability and soil microbiome alterations impacted via individual abundance.}, journal = {Biologia futura}, volume = {76}, number = {3}, pages = {399-411}, pmid = {40478395}, issn = {2676-8607}, support = {CI2021A04012//CACMS Innovation Fund/ ; ZZ16-YQ-04//Fundamental Research Funds of CACMS/ ; H2023406026//Hebei Natural Science Foundation/ ; QN2024119//Science Research Project of Hebei Education Department/ ; }, mesh = {Animals ; *Soil Microbiology ; *Microbiota/physiology ; *Bufonidae/microbiology/physiology ; }, abstract = {Artificial breeding is a valid strategy for the reverse of current extinction tendency in wild population of amphibian like toads. Considering public health, an alternative to antibiotics is demanded for ameliorating survival of toads during the culture period. Relying on the cognition of probiotics or antagonistic bacteria, the present work investigated viability and soil microorganism variations induced by distribution characteristic on toads using high-throughput sequencing technology. Comparison and analysis of soil metagenome from clustered and depopulated groups distinguished by toad behavior showed differences of bacterial community composition (e.g., Proteobacteria bacterium TMED72 and Nannocystis exedens) and antibiotic resistance genes involving antibiotic efflux and inactivation (e.g., mdtB and acrF). There were 18 and 10 distribution-typical genes independently enriched in Proteobacteria bacterium TMED72 and bacterium TMED88 of clustered group and Nannocystis exedens of depopulated group. In Nannocystis exedens, one of the distribution-typical genes was annotated as 6-phosphogluconate dehydrogenase acting role on bacterial growth restriction. It implied that, compared with the group emerging rare traces, the reduction of soil bacteria which possess genes retarding bacterial growth putatively impairs competitiveness to pathogenic bacteria and results in poor survivability of toads under clustering behavior. With the co-occurrence of virulence genes, more evidences are needed on the antagonistic bacteria Nannocystis exedens as antibiotic substitute.}, } @article {pmid40325330, year = {2025}, author = {Panicucci, C and Casalini, S and Fiorito, G and Rinaldi, AB and Biagioli, V and Cangelosi, D and Brolatti, N and Principi, E and Baratto, S and Pedemonte, M and Morando, S and Riva, A and Venturino, C and Striano, P and Uva, P and Bruno, C}, title = {Exploratory Analysis of Gut Microbiota Profile in Duchenne Muscular Dystrophy (DMD) Patients with Intellectual Disability.}, journal = {Molecular neurobiology}, volume = {62}, number = {9}, pages = {11799-11809}, pmid = {40325330}, issn = {1559-1182}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Intellectual Disability/microbiology/complications ; *Muscular Dystrophy, Duchenne/microbiology/complications ; Adolescent ; Male ; Child ; Female ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; }, abstract = {This study investigates the differences in gut microbiota composition between DMD patients with (DMD +) and without (DMD -) intellectual disability (ID) and its potential role in cognitive outcomes. In this study, we assessed the gut microbiota in 50 genetically confirmed DMD patients (median age 13.1 years) using 16S rRNA gene sequencing. Cognitive assessment was performed using the Wechsler Intelligence Scales, with ID defined as an IQ < 70. Stool samples were analyzed, and statistical methods were used to assess alpha- and beta-diversity. Thirty-four percent of patients had ID. No significant differences were found in alpha-diversity or in the Firmicutes/Bacteroidetes ratio. However, beta-diversity analysis revealed significant differences between DMD + and DMD - groups, including, in DMD + , an increased abundance of Propionibacterium and Bifidobacterium, and a reduction in Bulleidia. These bacteria are involved in metabolic pathways that can influence neurological health through the gut-brain axis, particularly via the production of short-chain fatty acids. While these preliminary findings suggest a possible association between gut microbiota profile and cognitive impairment in DMD, further research is needed to explore a causal relationship and consider microbiota-targeted therapeutic strategies.}, } @article {pmid40254787, year = {2025}, author = {Dame-Teixeira, N and Lynch, J and Yu, X and Cena, JA and Do, T}, title = {The Caries and Caries-Free Archaeome.}, journal = {Journal of dental research}, volume = {104}, number = {10}, pages = {1138-1146}, doi = {10.1177/00220345251329343}, pmid = {40254787}, issn = {1544-0591}, mesh = {*Dental Caries/microbiology ; Humans ; *Archaea/genetics/isolation & purification/classification ; *Dental Plaque/microbiology ; *Saliva/microbiology ; Metagenomics ; Microbiota ; }, abstract = {The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.}, } @article {pmid40830497, year = {2025}, author = {Marialva, EF and Martins-Campos, KM and de Almeida, VR and Ríos-Velasquez, CM and Tempone, AJ and Pessoa, FAC and Traub-Cseko, YM}, title = {Investigation of bacterial microbiota variability in two allopatric populations of Nyssomyia umbratilis, susceptible and nonsusceptible to Leishmania (Viannia) guyanensis infection in the Amazon region.}, journal = {Parasites & vectors}, volume = {18}, number = {1}, pages = {354}, pmid = {40830497}, issn = {1756-3305}, mesh = {Animals ; *Psychodidae/microbiology/parasitology ; Brazil ; Female ; *Leishmania guyanensis/physiology ; *Insect Vectors/microbiology/parasitology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Humans ; }, abstract = {BACKGROUND: Sand flies of the species Nyssomyia umbratilis (Diptera: Psychodidae: Phlebotominae) are vectors of the parasite Leishmania (Viannia) guyanensis, one of the etiological agents of cutaneous leishmaniasis in the Amazon region. In addition, Ny. umbratilis is a cryptic species, with populations showing differences in their ability to transmit the parasite. For instance, populations of Ny. umbratilis from the Manacapuru municipality (MAN), located on the south bank of the Negro river, in the Amazonas state of Brazil, shows refractoriness to Leishmania infection, while populations from Rio Preto da Eva municipality (RPE), located on the north bank of the Negro river, are susceptible to infection. This lack of vectorial capacity may be caused by several factors, including the intestinal bacterial microbiota of sand flies.

METHODS: In this work, we carried out a metagenomic study of the intestinal microbiota of Ny. umbratilis populations from MAN and RPE. Ny. umbratilis females were collected in forested areas, sand fly midguts were dissected, DNA was extracted, and the 16 S rRNA gene sequenced to identify the bacterial composition of the microbiota.

RESULTS: In total, 16 phyla, 33 classes, 49 orders, 93 families, and 112 genera of bacteria were identified. The phylum Proteobacteria was the most frequent (85.9%) in both localities, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes with, 9.9%, 4.9%, and 4.4%, respectively. In MAN, 84 genera were identified and 79 in RPE, with MAN having a greater richness compared with RPE. Among these, the genera Rickettsia, Prevotella, Porphyromonas, Peptostreptococcus, and Caulobacter were the most prevalent in MAN, and the genera Rickettsia, Prevotella, Cryocola, Porphyromonas, and Caulobacter were the most prevalent in RPE.

CONCLUSIONS: Bacterial microbiota from MAN insects presents a greater diversity in relation to the RPE insects. Some of the identified bacteria have the potential to be used in alternative transmission control approaches as the development of transgenic vectors, and also, bacteria found exclusively in MAN sand flies may be candidates for a future transmission control approach to combat leishmaniasis in the Amazon region.}, } @article {pmid40829558, year = {2025}, author = {Huang, WC and Spang, A}, title = {DPANN archaea.}, journal = {Current biology : CB}, volume = {35}, number = {16}, pages = {R791-R794}, doi = {10.1016/j.cub.2025.06.038}, pmid = {40829558}, issn = {1879-0445}, mesh = {*Archaea/genetics/physiology/classification/metabolism ; *Symbiosis ; Phylogeny ; *Genome, Archaeal ; Biological Evolution ; }, abstract = {Archaea are one of the two primary domains of life alongside Bacteria. Extant archaea play an important role in global nutrient cycles and comprise members that were crucial for the evolution of life on Earth including the origin of eukaryotic cells through a symbiotic integration of an archaeal and bacterial partner. Despite their importance in ecology and evolution, our knowledge of archaeal diversity and function remains limited in part because it has proven challenging to cultivate archaea in the laboratory. Over the last two decades, the use of novel cultivation-independent approaches such as metagenomics has not only led to the discovery of a vast diversity of previously unknown archaeal lineages but also provided a window into their genomic content, allowing researchers to make predictions about metabolic functions and lifestyles. For example, by combining genomics approaches with phylogenetic analyses (that is, the reconstruction of species trees) researchers have uncovered several phylum-level lineages of putative genome-reduced archaea referred to as the 'DPANN' archaea, whose members were shown to have limited metabolic capabilities, indicating their dependency on symbiotic partners. These findings are consistent with observations from cultivation-based studies that have succeeded in enriching some of these small-cell symbionts in co-cultures with their hosts. Although they were initially discovered in extreme environments, DPANN archaea have now been shown to be widespread across a variety of environments and may thus play an important role in not only host evolution but also ecology. Herein, we aim to highlight DPANN archaea by providing an overview of their diversity, genomic and metabolic features, unique cell biology and interactions, and evolutionary origins. We also underscore several fascinating topics that remain underexplored.}, } @article {pmid40254701, year = {2025}, author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K}, title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40254701}, issn = {1867-1314}, abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.}, } @article {pmid39966546, year = {2025}, author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and Mihula, M and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M}, title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.}, journal = {Pediatric research}, volume = {97}, number = {7}, pages = {2267-2271}, pmid = {39966546}, issn = {1530-0447}, mesh = {Humans ; Female ; *Milk, Human/immunology/chemistry ; Pregnancy ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects ; *Immunoglobulin A/metabolism ; Case-Control Studies ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Translational Research, Biomedical ; *Microbiota/drug effects ; Adult ; *Prenatal Exposure Delayed Effects ; }, abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.

METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.

RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.

CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.

IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.}, } @article {pmid32564244, year = {2020}, author = {Mokkala, K and Houttu, N and Koivuniemi, E and Sørensen, N and Nielsen, HB and Laitinen, K}, title = {GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {16}, number = {7}, pages = {76}, pmid = {32564244}, issn = {1573-3890}, mesh = {Acetylglucosamine/blood ; Adult ; Biomarkers/blood ; C-Reactive Protein/metabolism ; Cardiovascular Diseases/blood/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; Female ; Fibrinogen/metabolism ; Gastrointestinal Microbiome/*physiology ; Glycoproteins/blood ; Haptoglobins/metabolism ; Humans ; Inflammation/blood/*metabolism ; Metabolomics/methods ; Obesity/blood/metabolism ; Pregnancy ; Serum Amyloid A Protein/metabolism ; }, abstract = {INTRODUCTION: Gut microbiota is, along with adipose tissue, recognized as a source for many metabolic and inflammatory disturbances that may contribute to the individual's state of health.

OBJECTIVES: We investigated in cross-sectional setting the feasibility of utilizing GlycA, a novel low grade inflammatory marker, and traditional low grade inflammatory marker, high sensitivity CRP (hsCRP), in reflecting serum metabolomics status and gut microbiome diversity.

METHODS: Fasting serum samples of overweight/obese pregnant women (n = 335, gestational weeks: mean 13.8) were analysed for hsCRP by immunoassay, GlycA and metabolomics status by NMR metabolomics and faecal samples for gut microbiome diversity by metagenomics. The benefits of GlycA as a metabolic marker were investigated against hsCRP.

RESULTS: The GlycA concentration correlated with more of the metabolomics markers (144 out of 157), than hsCRP (55 out of 157) (FDR < 0.05). The results remained essentially the same when potential confounding factors known to associate with GlycA and hsCRP levels were taken into account (P < 0.05). This was attributable to the detected correlations between GlycA and the constituents and concentrations of several sized VLDL-particles and branched chain amino acids, which were statistically non-significant with regard to hsCRP. GlycA, but not hsCRP, correlated inversely with gut microbiome diversity.

CONCLUSION: GlycA is a superior marker than hsCRP in assessing the metabolomic profile and gut microbiome diversity. It is proposed that GlycA may act as a novel marker that reflects both the gut microbiome and adipose tissue originated metabolic aberrations; this proposal will need to be verified with regard to clinical outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT01922791, August 14, 2013.}, } @article {pmid40825816, year = {2025}, author = {Kaushal, M and Kolombia, YA and Alakonya, AE and Masso, C}, title = {Comparing soil microbial diversity in smallholder plantain backyard gardens and main farms in Western and Central Africa.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {30220}, pmid = {40825816}, issn = {2045-2322}, support = {HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; }, abstract = {In sub-Saharan Africa (SSA), plantains (Musa spp.) are a staple crop and a vital source of income for smallholder farmers. Despite their importance, the microbial diversity of soils in plantain-growing agroecologies remains poorly understood-particularly how it may influence plant performance and resilience through soil-plant interactions. In this study, we used Illumina MiSeq-based 16S rDNA sequencing to characterize bacterial communities in the rhizosphere of plantains cultivated under two distinct agroecological settings: Backyard gardens and main farms. Analyses of alpha and beta diversity (Sobs, Chao1, ACE, Shannon-Wiener, and Simpson indices; P < 0.05) revealed significant differences in species richness and community structure between the two agroecologies. Actinobacteria (55%) emerged as the dominant phylum, followed by Proteobacteria (21%) and Acidobacteria (15%). Beneficial genera such as Bacillus, Streptomyces, Bradyrhizobium, and Paenibacillus were also detected. Functional predictions based on COG and KEGG databases indicated notable differences in microbial functional potential between the two settings. These results suggest that agroecological context and habitat type strongly influence rhizosphere microbial diversity, with important implications for enhancing plant-microbe interactions and supporting crop resilience in SSA's resource-limited smallholder systems.}, } @article {pmid40817036, year = {2025}, author = {Chen, Y and Huang, S and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W}, title = {Viral metagenomics reveals parvovirus dark matter of herbivorous wildlife from the Qinghai-Tibet Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {508}, pmid = {40817036}, issn = {1471-2180}, support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; }, abstract = {BACKGROUND: As one of the birthplaces of modern biodiversity, the Qinghai-Tibet Plateau is home to a rich variety of unique animal groups. Herbivorous wildlife constitutes a vital component of the plateau's ecosystems, yet current research on parvoviruses in these species remains limited. With the development of viral metagenomics and next-generation sequencing technology, more and more novel viruses have been detected.

RESULTS: In this study, we collected 741 fecal samples from herbivorous wildlife across three distinct habitats on the Qinghai-Tibet Plateau and employed metagenomics analysis technology to characterize the parvovirus dark matter. We identified 32 parvoviruses by analysis, of which 13 were closely related to the members of Bocapavovirus, Dependoparvovirus and Protoparvovirus in the subfamily of Parvovirinae, 5 belonging to the Densovirinae subfamily, and 5 were classified into the newly proposed subfamily of Hamaparvovirinae. Additionally, 9 parvoviruses remain unclassified and cannot be assigned to any existing subfamily. We conducted a phylogenetic analysis based on the non-structural proteins of the viruses to explore the evolutionary relationships among parvoviruses, and found that some viruses could not be clustered with known parvoviruses.

CONCLUSIONS: These results enrich our understanding of parvovirus and viral dark matter, and reveal that these wild animals carry a large number of unknown new viruses that may have implications for the ecological balance of the Qinghai-Tibet Plateau.}, } @article {pmid40796349, year = {2025}, author = {Huang, WC and Probst, M and Hua, ZS and Szánthó, LL and Szöllősi, GJ and Ettema, TJG and Rinke, C and Williams, TA and Spang, A}, title = {Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf201}, pmid = {40796349}, issn = {1537-1719}, abstract = {The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focused on characterising the diversity of Asgard archaea in an effort to identify the closest extant relatives of eukaryotes. However, resolving archaeal phylogeny is challenging, and the positions of two recently-described lineages - Njordarchaeales and Panguiarchaeales - are uncertain, in ways that directly bear on hypotheses of early evolution. In initial phylogenetic analyses, these lineages branched either with Asgards or with the distantly-related Korarchaeota, and it has been suggested that their genomes may be affected by metagenomic contamination. Resolving this debate is important because these clades include genome-reduced lineages that may help inform our understanding of the evolution of symbiosis within Asgard archaea. Here, we performed phylogenetic analyses revealing that the Njordarchaeales and Pangiuarchaeales constitute the new class Njordarchaeia within Asgard archaea. We found no evidence of metagenomic contamination affecting phylogenetic analyses. Njordarchaeia exhibit hallmarks of adaptations to (hyper-)thermophilic lifestyles, including biased sequence compositions that can induce phylogenetic artifacts unless adequately modelled. Panguiarchaeum is metabolically distinct from its relatives, with reduced metabolic potential and various auxotrophies. Phylogenetic reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood-Ljungdahl pathway. The subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle potentially based on H2-syntrophy. Thus, Panguiarchaeum may contain the first obligate symbionts within Asgard archaea.}, } @article {pmid40795932, year = {2025}, author = {Teng, ZJ and Yuan, XJ and Liu, R and Xu, SC and Chen, XL and Chen, Y and Zhang, YZ}, title = {Inositol phosphates as an overlooked phosphorous source in marine ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf161}, pmid = {40795932}, issn = {1751-7370}, abstract = {Inositol phosphates, common phosphorus storage compounds that are also crucial for eukaryotic cell signaling, constitute a significant portion of dissolved organic phosphorus in coastal waters. The hydrolysis of inositol phosphates could be an important contributor to phosphorus cycling in phosphorus-limited marine ecosystems, yet this process remains poorly understood in marine contexts. In this study, we reveal substantial concentrations of Inositol phosphates in marine macrophytes, including green, brown, and red algae as well as common seagrasses, suggesting that these organisms are likely major biological sources of inositol phosphates in the oceans. A comprehensive analysis of genes involved in inositol phosphates hydrolysis in global marine metagenomes and metatranscriptomes identified key roles for γ-, α-, and δ-proteobacteria, with additional contributions from Flavobacteriia. The degradation of marine inositol phosphates was predominantly mediated by alkaline β-propeller phytases, though genes associated with acidic cysteine phytases and purple acid phytases were also widely present. Community structure and functional traits linked to inositol phosphates degradation were shaped largely by stochastic processes. Further examination of enzyme activity at the protein and community levels indicated that phytate metabolism by marine microbes is likely a widespread phenomenon in the ocean. Overall, this study highlights inositol phosphates hydrolysis as an essential yet overlooked adaptation by marine microorganisms to address phosphorus limitations in ocean ecosystems.}, } @article {pmid40795730, year = {2025}, author = {D'Ugo, E and Mukherjee, A and Resitano, M and Giuseppetti, R and Fortini, D and Bruna Matturro, and Chirico, M and Pisanu, ME and Tucci, M and Pozzi, R and Lovecchio, N and Slawomir, O and Iosi, F and Villa, L and Iorio, E and Aulenta, F and Viggi, CC and Bertuccini, L and Magurano, F}, title = {Fishing out microorganisms for bioremediation using metagenomics: Isolation and whole-genome sequencing of the metabolically versatile Rhodococcus erythropolis LP27217 strain from oil spill lake.}, journal = {Journal of hazardous materials}, volume = {496}, number = {}, pages = {139463}, doi = {10.1016/j.jhazmat.2025.139463}, pmid = {40795730}, issn = {1873-3336}, abstract = {Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.}, } @article {pmid40794955, year = {2025}, author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D}, title = {Decoding longitudinal microbiome trajectories: an interpretable machine learning approach for biomarker discovery and prediction.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40794955}, issn = {1477-4054}, support = {R03 DE034507/DE/NIDCR NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; U01DE025046/NH/NIH HHS/United States ; 1R03DE034507-01/NH/NIH HHS/United States ; }, mesh = {Humans ; *Machine Learning ; *Biomarkers ; *Microbiota ; Longitudinal Studies ; Gastrointestinal Microbiome ; }, abstract = {Information generated from longitudinally sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g. metagenomics) poses analytical challenges.To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g. XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa, but also offers improved prediction accuracy compared with existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. Moreover, LP-Micro highlights critical time points and associated microbial changes: oral microbial changes, including Streptococcus mutans, are most informative for predicting childhood dental disease at around 39 months of age, while gut microbial changes shortly after bariatric surgery strongly predict future weight loss. These findings are both informative and aligned with clinical expectations. The tool LP-Micro can be seen at https://github.com/IV012/LPMicro.}, } @article {pmid40794299, year = {2025}, author = {El-Halim, HMA and El-Hadidi, M and Fouad, N and Hamed, RR and Megid, IA and Taha, MH and Radwan, KH}, title = {Metagenomic insight into drought-induced changes in the Egyptian wheat rhizosphere microbiome.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {8}, pages = {310}, pmid = {40794299}, issn = {1573-0972}, mesh = {*Triticum/microbiology ; *Rhizosphere ; *Droughts ; Egypt ; *Microbiota/genetics ; Soil Microbiology ; Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Stress, Physiological ; RNA, Ribosomal, 16S/genetics ; Metagenome ; }, abstract = {Wheat is one of the most important cereal crops and an important source of food for billions of people worldwide. However, drought stress can pose a real threat to its productivity and lead to significant yield losses, especially in Egypt. The rhizospheric microbiome of wheat can play an important role in drought stress and help wheat to respond to this abiotic stress. Understanding this microbiome is therefore also important to improve drought stress resilience and productivity. In this study, a metagenomic analysis was performed to investigate how the composition and diversity of microbial communities associated with the wheat rhizosphere change under drought. Taxonomic and phylogenetic analyses revealed a shift in microbial abundance, with Actinobacteria, Bacteroidetes, Proteobacteria and Verrucomicrobia being the four most abundant phyla of the ethnic microbiota. Remarkably, other classes, including Alphaproteobacteria and Cytophagia, were significantly enriched under drought, which could be a promising enhancement of plant stress altruism. Differential abundance analysis showed that the control samples had higher abundance of microbial taxa such as OD1, WS2, Chlorobi, ABY1 and SHA-109 compared to the drought-treated genotypes. Functional prediction analysis using PICRUSt showed that an uncharacterized ATP-binding protein within the AAA + superfamily is overrepresented under drought conditions. This suggests that these genes may play a role in stress adaptation, possibly via energy-dependent regulation of cellular processes involved in plant survival. Our results expand our understanding of the complexity of responses of the wheat rhizosphere microbiome to drought and have practical implications for the development of microbial target combinations to improve wheat tolerance and productivity in the context of climate change challenges.}, } @article {pmid40792105, year = {2025}, author = {Han, W and Zhou, Y and Wang, Y and Liu, X and Sun, T and Xu, J}, title = {Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1591076}, pmid = {40792105}, issn = {2235-2988}, mesh = {Humans ; *Machine Learning ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics/methods ; *Feces/microbiology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy ; *Lung Neoplasms/immunology/microbiology/therapy/drug therapy ; Immunotherapy ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/genetics/drug effects ; }, abstract = {BACKGROUND: Substantial interstudy heterogeneity in cancer immunotherapy-associated biomarkers has hindered their clinical applicability. To address this challenge, we performed a comprehensive integration of publicly available global metagenomic datasets. By leveraging metagenomic profiling and machine learning approaches, this study aimed to elucidate gut microbial signatures associated with immune response in lung cancer (LC) and to evaluate the modulatory effects of antibiotic exposure.

METHODS: A systematic literature search was conducted to identify relevant datasets, resulting in the inclusion of 209 fecal metagenomic samples: 154 baseline samples (45 responders, 37 non-responders, and 72 healthy controls) and 55 longitudinal samples collected during immunotherapy. We performed taxonomic and functional characterization of gut microbiota (GM) differentiating responders from non-responders, delineated microbiome dynamics during treatment, and assessed the impact of antibiotics on key microbial taxa. Among eight machine learning algorithms evaluated, the optimal model was selected to construct a predictive framework for immunotherapy response.

RESULTS: Microbial α-diversity was significantly elevated in responders compared to non-responders, with antibiotic administration further amplifying this difference-most notably at the species level. Integrative multi-omics analysis identified two pivotal microbial biomarkers, s_Bacteroides caccae and s_Prevotella copri, which were strongly associated with immunotherapy efficacy. A random forest-based classifier achieved robust predictive performance, with area under the curve (AUC) values of 0.82 and 0.79 at the species and genus levels, respectively. Notably, P. copri was further enriched in responders with poor progression-free survival (PFS <3 months), indicating a potential deleterious role. Antibiotic exposure significantly influenced the abundance and functional potential of these key taxa. KEGG-based functional analysis revealed the enrichment of amino acid metabolism pathways in responders. Additionally, CARD database annotation demonstrated that the majority of antibiotic resistance genes were associated with Bacteroidetes and Proteobacteria, implicating these taxa in shaping microbial-mediated therapeutic responses.

CONCLUSIONS: This study represents the first large-scale, cross-cohort integration of metagenomic data to identify reproducible GM signatures predictive of immune checkpoint inhibitor efficacy in LC. The findings not only underscore the prognostic relevance of specific taxa but also establish a foundation for developing microbiome-informed, personalized immunotherapeutic strategies.}, } @article {pmid40790223, year = {2025}, author = {Ren, Y and Zhang, P and Yu, H and Li, S and Jiang, H}, title = {Metagenome-based characterization of the gut virome in patients with schizophrenia.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {895}, pmid = {40790223}, issn = {1479-5876}, support = {82170755//National Natural Science Foundation of China/ ; LHYYKYQD20240307//Scientif Research Foudation of People's Hospital of Longhua of Shenzhen/ ; }, mesh = {Humans ; *Schizophrenia/virology/microbiology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; *Metagenome/genetics ; Female ; Adult ; Feces/virology/microbiology ; Middle Aged ; Case-Control Studies ; }, abstract = {BACKGROUND: Schizophrenia (SCZ) is a multifactorial psychiatric disorder increasingly linked to gut microbial dysbiosis. While bacterial alterations have been widely studied, the role of the gut virome in SCZ remains largely unexplored. This study aimed to characterize the gut virome in SCZ and identify potential viral biomarkers associated with the disease.

METHODS: We analyzed fecal metagenomic data from 171 individuals (90 SCZ patients and 81 controls) using the Chinese Gut Virus Catalog (cnGVC). We assessed gut virome diversity, identified SCZ-associated vOTUs, explored virus-bacteria correlations, and evaluated diagnostic potential using random forest models. In addition, we examined follow-up samples from SCZ patients to assess the impact of antipsychotic treatment on the gut virome.

RESULTS: We identified 171 vOTUs that differed significantly between SCZ patients and controls, with 124 enriched in SCZ-mainly from Siphoviridae and Flandersviridae. Correlation analysis revealed altered virus-bacteria interactions in SCZ, including disease-specific associations with Akkermansia and Clostridia. A random forest classifier based on virome features achieved an AUC of 93.2%, outperforming the bacterial model. External validation using ASD and PD cohorts yielded lower AUCs (61.2-67.0%), suggesting disease specificity. In follow-up samples collected after three months of treatment, we observed partial changes in alpha diversity, while beta diversity remained stable, indicating that antipsychotic therapy may alter specific viral taxa without broadly reshaping the overall gut virome structure.

CONCLUSIONS: This study provides evidence of distinct gut virome alterations in SCZ and identifies specific viral markers with strong diagnostic potential. These findings highlight the underappreciated role of the gut virome in psychiatric disorders and support its utility as a non-invasive biomarker for SCZ diagnosis and future therapeutic development.}, } @article {pmid40790024, year = {2025}, author = {Kiguchi, Y and Hamamoto, N and Kashima, Y and Runtuwene, LR and Ishizaka, A and Kuze, Y and Enokida, T and Tanaka, N and Tahara, M and Kageyama, SI and Fujisawa, T and Yamashita, R and Kanai, A and Tuda, JSB and Mizutani, T and Suzuki, Y}, title = {Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7397}, pmid = {40790024}, issn = {2041-1723}, support = {22fk0108538s0201//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {Humans ; Saliva/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; *Mouth/microbiology ; Female ; Male ; Colorectal Neoplasms/microbiology ; Head and Neck Neoplasms/microbiology ; Metagenome ; Adult ; DNA, Bacterial/genetics ; *Bacteria/genetics ; Middle Aged ; Streptococcus/genetics ; }, abstract = {Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown. Here, we discover a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly. Even though this ECE family was not hitherto identified, our global prevalence analysis using 476 salivary metagenomic datasets elucidates that these ECEs reside in 74% of the population. These ECEs, which we named, "Inocles", are giant plasmid-like circular genomic elements of 395 kb in length, including Streptococcus as a host bacterium. Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells. Moreover, Inocles exhibit significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examine and find their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment.}, } @article {pmid40788706, year = {2025}, author = {Israel, A and Israel, S and Weizman, A and Ashkenazi, S and Vinker, S and Magen, E and Merzon, E}, title = {Atovaquone-proguanil and reduced digestive cancer risk: a Toxoplasma gondii connection.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2545412}, pmid = {40788706}, issn = {1949-0984}, mesh = {Humans ; Middle Aged ; *Atovaquone/therapeutic use/pharmacology ; *Toxoplasma/isolation & purification/drug effects/genetics ; Adult ; Male ; Aged ; Female ; Retrospective Studies ; *Proguanil/therapeutic use/pharmacology ; Drug Combinations ; Gastrointestinal Microbiome/drug effects ; Feces/parasitology/microbiology ; *Colorectal Neoplasms/epidemiology/prevention & control/parasitology ; Toxoplasmosis ; Incidence ; Metagenomics ; }, abstract = {Emerging evidence suggests microbial pathogens contribute to digestive cancer risk. Atovaquone - proguanil (A-P), an antimalarial with antiparasitic activity, has been associated with a reduced risk of colorectal cancer (CRC). We conducted a retrospective cohort study using the TriNetX US Collaborative Network, including over 100,000 individuals aged 40-69 years who received A-P, matched 1:1 to controls who received other medications. Incident digestive cancers were analyzed using Cox proportional hazards models. Additionally, we performed a metagenomic analysis of 1,044 fecal samples from 156 individuals to assess the abundance of Toxoplasma gondii in CRC-associated microbiota. A-P use was associated with a significant reduction in digestive cancer incidence across all age groups: hazard ratios (HRs) ranged from 0.49 to 0.53 (all p < 0.001). Protective associations extended to pancreatic cancer (HR range, 0.50-0.72). In metagenomic analysis, T. gondii was the most discriminatory microbial species for CRC (p = 1.8 × 10[-16]), detected above threshold in 22.6% of CRC samples versus 1.6% of controls (odds ratio 18.2, 95% CI, 8.2-47.6, p = 2.3 × 10[-22]). These findings suggest T. gondii may be an overlooked microbial risk factor for digestive cancers, and that A-P may offer chemopreventive effects through antiparasitic activity. Prospective studies are needed to evaluate its preventive potential.}, } @article {pmid40785047, year = {2025}, author = {Shi, H and Wu, M and Wu, X and Liu, Z and Jiang, S and Li, G and Yang, Y and Fu, Y and Wang, Q and Zhang, G and Cheng, L}, title = {Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2542384}, pmid = {40785047}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Atherosclerosis/microbiology/genetics/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Transcriptome ; Metabolomics ; Multiomics ; }, abstract = {Atherosclerosis (AS), a predominant contributor to global cardiovascular disease burden, exhibits complex interplay with gut microbiota dysbiosis. While the associations between microbial imbalance and AS pathogenesis are well-documented, the pathophysiological mechanisms governing microbe-host crosstalk remain incompletely characterized. Current research limitations stem from methodological heterogeneity across studies and the absence of consensus regarding disease-specific microbial signatures. In this study, we conducted an integrated multi-omics analysis to characterize the functional signatures of gut microbiome in AS. We collected all public AS-related 6 microbiome datasets and 8 peripheral blood host transcriptomic datasets from across the world, comprising 456 metagenomic samples and 111 16S rRNA gene sequencing samples for microbial profiling, alongside 118 RNA-Seq samples and 302 microarray samples. We systematically characterized AS microbial taxa and computationally inferred the metabolic potential for the gut microbiome using metabolomic-related data. Metabolite-host gene interactions were further predicted based on the synergistic effects between microbiome and host transcriptome in AS. Five "microbe-metabolite-host gene" tripartite associations related to AS were identified involving 5 microbial genera (Actinomyces, Bacteroides, Eisenbergiella, Gemella, and Veillonella), 2 metabolites (Ethanol and H2O2), and 2 host genes (FANCD2 and GPX2), and the reliability of these associations was validated. Five microbial genera demonstrated robust diagnostic potential as noninvasive biomarkers, with 5-fold cross-validation, study-to-study transfer validation, and leave-one-study-out (LOSO) validation confirming good diagnostic performance. Additionally, the specificity of the biomarkers was validated against hypertension, inflammatory bowel disease (IBD), diabetes, and obesity cohorts. Our study unveiled the functional characteristics of gut microbiota interacting with AS host genes and highlighted the potential of gut microbiota as both diagnostic biomarkers and therapeutic targets for AS. However, the findings should be interpreted considering the inherent heterogeneity of the integrated datasets and the preliminary diagnostic value of the biomarkers.}, } @article {pmid40784769, year = {2025}, author = {Kim, HS and Kim, BH and Nam, B and Oh, SJ and Park, SK and Lee, SW and Lee, JY and Jo, S and Lee, YA and Lee, JY and Park, DI and Kim, TH and Lee, CK}, title = {Oral-gut microbiome axis in a Korean cohort with inflammatory bowel disease and ankylosing spondylitis (INTEGRATE): a prospective and observational study protocol.}, journal = {BMJ open}, volume = {15}, number = {8}, pages = {e092075}, pmid = {40784769}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; *Spondylitis, Ankylosing/microbiology ; Republic of Korea ; Observational Studies as Topic ; *Crohn Disease/microbiology ; RNA, Ribosomal, 16S ; *Inflammatory Bowel Diseases/microbiology ; Female ; Adult ; *Mouth/microbiology ; Dysbiosis ; Male ; *Colitis, Ulcerative/microbiology ; Saliva/microbiology ; }, abstract = {INTRODUCTION: The global burden of chronic immune-mediated inflammatory diseases (IMIDs) is increasing, and rising prevalence rates significantly affect socioeconomic factors and quality of life. Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), along with ankylosing spondylitis (AS), are prominent chronic IMIDs that share overlapping pathophysiological mechanisms. Recent research has highlighted the importance of the gut microbiota in the pathogenesis of these diseases, suggesting that shared microbial dysbiosis may contribute to their development. Comprehensive research focusing on the gut and oral microbial characteristics and environmental factors is essential to elucidate the fundamental pathophysiology and develop personalised management strategies for IBD and AS. In-depth analyses and insights based on multiomics approaches are required to achieve these objectives.

METHODS AND ANALYSIS: This protocol describes a nationwide prospective observational study of CD, UC and AS in a Korean population. Over 5 years, we aim to recruit at least 900 patients with IBD and 200 first-degree relatives (FDRs), 500 patients with AS and 200 of their FDRs, and 2244 healthy controls. We will systematically collect clinical data and biological samples, including saliva, stool, blood and tissue biopsies, for integrative multiomics analyses focusing primarily on the microbiome. Highly advanced full-length 16S ribosomal RNA gene sequencing and shotgun metagenomics will be used to characterise the microbial composition of saliva and stool samples. Quantitative microbiome profiling will be used to address the pathological, physiological and ecological differences between microbial groups that may be masked by their relative abundance. Metabolomic analyses will be conducted on saliva, stool and plasma samples to assess functional metabolic profiles. Culturomics will be used to isolate, identify and characterise the diversity of microbial species, including rare or previously unrecognised species, to provide a comprehensive understanding of the microbiota associated with these diseases.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the Ethics Committee of Kyung Hee University Hospital, Hanyang University Hospital, Kangbuk Samsung Hospital, Yeungnam University Hospital, Kyungpook National University Hospital, Chonnam National University Hospital, Wonkwang University Hospital, Catholic University Daejeon St. Mary's Hospital, Soon Chun Hyang University Hospital Cheonan, Chung-Ang University Hospital, Inje University Haeundae Paik Hospital, Dankook University Hospital, Hanyang University Guri Hospital, Kyung Hee University Hospital at Gangdong, Chung-Ang University Gwangmyeong Hospital and Keimyung University Dongsan Hospital. Our research team will provide detailed information about the study, including an information sheet explaining its aims and procedures, prior to enrolment. Prospective participants will be informed that they have the right to withdraw from the study at any time, without penalty. Participants will be assured of the anonymity and confidentiality of any data they provide throughout the study, using participant numbers and the storage of sensitive data in locked cabinets. Participants will be enrolled in the study only after providing written informed consent to the research staff. The results of this study will be disseminated to healthcare and academic professionals through publications in peer-reviewed journals and presentations at international conferences.

TRIAL REGISTRATION NUMBER: This prospective observational study is registered at ClinicalTrials.gov ((ID: NCT06124833, data first posted: 9 November 2023); (ID: NCT06076083, data first posted: 21 November 2023) and (ID: NCT06183697, data first posted: 27 December 2023)).}, } @article {pmid40783398, year = {2025}, author = {Shen, Y and Sun, D and Chen, K and Jiang, J and Shao, D and Yang, L and Sun, C and Liu, D and Ke, Y and Wu, C and Walsh, TR and Shen, J and Lv, Z and Wang, Y}, title = {High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {156}, pmid = {40783398}, issn = {2055-5008}, support = {81991535//National Natural Science Foundation of China/ ; 32141002//National Natural Science Foundation of China/ ; 2022YFD1800400//National Key Research and Development Program of China/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Dietary Fiber/administration & dosage ; *Diet, High-Fat ; Mice ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Metagenomics/methods ; Male ; Humans ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Interspersed Repetitive Sequences ; Female ; }, abstract = {Antimicrobial resistance (AMR) is a global health challenge. The gut microbiome, a major reservoir for AMR, is influenced by dietary habits. However, the specific impact of dietary patterns on gut resistome remains poorly understood. This study aimed to assess the effects of high-fat/low-fiber and high-fiber/low-fat diets on the development of AMR in the gut microbiome. The shift from a normal diet to a high-fat/low-fiber or a high-fiber/low-fat diet in mice resulted in corresponding increases and decreases in the relative abundance of the resistome (0.14 to 0.25, p < 0.001 vs. 0.14 to 0.09 p < 0.05), virulence genes (VGs) (0.56 to 0.91, p < 0.001 vs. 0.58 to 0.50, p < 0.05), and mobile genetic elements (MGEs) (0.20 to 1.66, p < 0.001 vs. 0.22 to 0.13, p < 0.05), respectively. Network analyses identified bacteria such as Bacteroides, Parabacteroides, and Alistipes as hosts of ARGs and VGs, with changes in their abundance closely associated with shifts in ARG and VG levels. Mobile genetic elements such as Tn916, ISBf10, IS91, and intl1 were linked to these variations, including genes conferring resistance to vancomycin and capsule-related VGs. In humans, a similar trend was observed, with high-fat diets correlating with higher resistome levels, while high-fiber diets were associated with lower resistome levels compared to a normal diet group. ARGs were more prevalent in pathogenic genera such as Enterococcus spp., Klebsiella spp., Pseudomonas spp., and Staphylococcus spp. The high-fat/low-fiber diet increased the bacterial resistome and VG abundance compared to a high-fiber/low-fat diet. Therefore, adopting a high-fiber/low-fat diet may be an effective strategy to reduce the AMR burden in the human gut, providing a valuable insight for public health recommendations.}, } @article {pmid40782126, year = {2025}, author = {Andeta, AF and Lema, NK and Debel, GL and Misganaw, FW and Ifa, AC}, title = {Evaluating food safety of traditionally fermented kocho: microbial profiling through classical methods and PacBio SMRT sequencing technology.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {9}, pages = {127}, pmid = {40782126}, issn = {1572-9699}, support = {CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; }, mesh = {*Fermented Foods/microbiology ; *Food Safety ; *Bacteria/classification/genetics/isolation & purification ; *Food Microbiology ; Ethiopia ; Fermentation ; Cross-Sectional Studies ; Fungi/isolation & purification/classification/genetics ; Microbiota ; }, abstract = {Enset (Ensete ventricosum) serves as a staple or co-staple food crop for over 20 million people in Southern, Southwestern, and Central Ethiopia, significantly contributing to regional food security. Despite its importance, food safety concerns surrounding its fermented product, kocho, remain largely unaddressed. This study aimed to evaluate the food safety of traditionally fermented kocho samples collected from districts in the Gamo Zone using a cross-sectional study design. The microbial community composition was analyzed through both culture-based methods and PacBio sequencing. The physicochemical properties exhibited slight variations in acidity, fermentation stage, and moisture content among samples from different districts. Culture-based microbiological analysis indicated total viable aerobic counts ranging from 5.76 to 7.13 log CFU/g, yeast and mold counts between 5.20 to 8.53 log CFU/g, and Enterobacteriaceae counts ranging from 5.03 to 6.13 log CFU/g. Metagenomic analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, with Acetobacter and Lactobacillus as the most prevalent genera. Notably, potential pathogenic bacteria, including Klebsiella pneumoniae, Klebsiella terrigena, Dysgonomonas capnocytophagoides, and Clostridium paraputrificum, were identified. The coexistence of beneficial microorganisms and potential pathogens underscores the urgent need for enhanced food safety measures in the traditional production of kocho.}, } @article {pmid40777923, year = {2025}, author = {Ramos, SF and Siguenza, N and Zhong, W and Mohanty, I and Lingaraju, A and Richter, RA and Karthikeyan, S and Lukowski, AL and Zhu, Q and Nunes, WDG and Zemlin, J and Xu, ZZ and Hasty, J and Dorrestein, PC and Panda, S and Knight, R and Zarrinpar, A}, title = {Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects.}, journal = {Cell host & microbe}, volume = {33}, number = {7}, pages = {1057-1072}, pmid = {40777923}, issn = {1934-6069}, support = {R01 EB030134/EB/NIBIB NIH HHS/United States ; R01 HL148801/HL/NHLBI NIH HHS/United States ; I01 BX005707/BX/BLRD VA/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA236352/CA/NCI NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; R01 AI163483/AI/NIAID NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 CA265719/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; R01 DK136117/DK/NIDDK NIH HHS/United States ; R01 CA258221/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Circadian Rhythm ; Mice ; Cecum/microbiology ; *Transgenes ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; *Transcriptome ; Diet, High-Fat ; Metagenomics ; Metagenome ; Mice, Inbred C57BL ; Male ; *Bacteria/genetics/metabolism ; Gene Expression Profiling ; }, abstract = {Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF). We show that metatranscriptomics uncover TRF-induced time-dependent microbial functional shifts that are undetectable with metagenomics alone. We also found bile salt hydrolase (bsh) from Dubosiella newyorkensis exhibits diurnal expression in the TRF group. Engineering this bsh, along with other candidates, into a native E. coli chassis reveals distinct differences in deconjugation and amidation activities, underscoring functional specificity. In vivo, a D. newyorkensis bsh improves insulin sensitivity, glucose tolerance, and body composition, suggesting a direct role in TRF metabolic benefits. This study highlights how coupling metatranscriptomics with engineered bacterial systems is a powerful approach for uncovering time-dependent bacterial functions related to health and disease.}, } @article {pmid40776036, year = {2025}, author = {Upadhyay, U and Dhar, E and Bomrah, S and Syed-Abdul, S}, title = {Unraveling the Role of Gut Microbiota in Colorectal Cancer: A Global Perspectives and Biomarkers as Early Screening Tool for Colorectal Cancer.}, journal = {Studies in health technology and informatics}, volume = {329}, number = {}, pages = {1145-1149}, doi = {10.3233/SHTI251018}, pmid = {40776036}, issn = {1879-8365}, mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; *Biomarkers, Tumor ; Metagenomics ; }, abstract = {Colorectal cancer (CRC), the second deadliest cancer globally, is closely tied to gut microbiota, opening doors for early detection and treatment. This review of 45 studies (2018-2024) highlights microbial biomarkers like Fusobacterium nucleatum, Bacteroides fragilis, and Parvimonas micra, with strong diagnostic accuracy (AUC >80%) across populations. Techniques like 16S rRNA sequencing, metagenomics, and shotgun sequencing revealed these links. Gut-based diagnostics offer a non-invasive, cost-effective alternative to colonoscopy and FIT for spotting early CRC and precancerous lesions. Yet, regional microbial differences and inconsistent methods-sample processing and sequencing-hinder comparability. Standardizing approaches and exploring fungi and viruses are key to unlocking microbiota's full potential in CRC prevention, diagnosis, and therapy.}, } @article {pmid40775451, year = {2025}, author = {Crognale, S and Amalfitano, S and Casentini, B and Di Pippo, F and Fazi, S and Tonanzi, B and Rossetti, S}, title = {Microbial signature of groundwater mixing in geothermal areas: insights from the Cimino-Vico volcanic system (central Italy).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {28941}, pmid = {40775451}, issn = {2045-2322}, support = {CN_00000033//Ministero dell'Università e della Ricerca/ ; CN_00000033//Ministero dell'Università e della Ricerca/ ; }, mesh = {*Groundwater/microbiology ; Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Hot Springs/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The complex structure and dynamics of geothermal ecosystems strongly affect the spatial distribution and activity of aquatic microbial communities. The interactions between groundwaters and thermal waters represent an additional selective factor. A deeper understanding of microbial diversity, metabolic potential, and ecological interactions in groundwater mixing zones is essential for evaluating their impact on biogeochemical cycles (such as sulfur, nitrogen, and carbon) and predicting the ecological consequences of water mixing on ecosystem functioning. In this study, the taxonomic diversity and metabolic potentialities of microbial communities in groundwater and thermal waters revealed the occurrence of novel thermophiles able to cope with extreme physical-chemical conditions and high concentrations of toxic elements, such as arsenic, characteristics of the studied area. Furthermore, a core microbiome composed of the families Burkholderiaceae, Caulobacteraceae, Halothiobacillaceae, and Sulfurovaceae was identified as markers of the interaction between the two water compartments. Our findings emphasize the key role of microbial communities in S-, As-, and N-related biogeochemical cycles of geothermal areas.}, } @article {pmid40774824, year = {2025}, author = {Lee, I and Kim, BS and Suk, KT and Lee, SS}, title = {Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2406017}, pmid = {40774824}, issn = {1738-8872}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; Humans ; Fecal Microbiota Transplantation ; *Enterobacteriaceae Infections/prevention & control/microbiology/therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Carbapenems/pharmacology ; Antimicrobial Stewardship ; }, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent a critical antimicrobial resistance threat due to their resistance to last-resort antibiotics and high transmission potential. While conventional strategies-such as infection control, antimicrobial stewardship, and novel antibiotic development-remain essential, growing attention has shifted toward the gut microbiome, which plays a central role in mediating colonization resistance against CRE. Disruption of the intestinal microbiota-primarily driven by antibiotic exposure and further exacerbated by non-antibiotic drugs such as proton pump inhibitors-reduces microbial diversity and impairs functional integrity, facilitating CRE acquisition, prolonged carriage, and horizontal transmission. In response, microbiome-based strategies-including microbiome disruption indices (MDIs), fecal microbiota transplantation (FMT), and rationally designed symbiotic microbial consortia-are being explored as novel approaches for CRE prevention and decolonization. Mechanistic studies have shown that colonization resistance is mediated by both direct mechanisms (e.g., nutrient competition, short-chain fatty acid production) and indirect mechanisms (e.g., immune modulation via IL-36 signaling). Advances in metagenomics, metabolomics, and culturomics have enabled high-resolution profiling of gut microbial communities and their functional roles. Emerging preclinical and clinical evidence supports the potential of microbiome-informed interventions to predict infection risk, enhance antimicrobial stewardship, and guide the development of next-generation probiotics targeting CRE. Longitudinal studies continue to evaluate the efficacy of FMT and synthetic microbial consortia in eradicating intestinal CRE colonization. Collectively, these insights underscore the promise of gut microbiome science as a complementary and innovative strategy for CRE control in the post-antibiotic era.}, } @article {pmid40772811, year = {2025}, author = {Ascari, R and Migliorati, S and Ongaro, A}, title = {A New Dirichlet-Multinomial Mixture Regression Model for the Analysis of Microbiome Data.}, journal = {Statistics in medicine}, volume = {44}, number = {18-19}, pages = {e70220}, pmid = {40772811}, issn = {1097-0258}, support = {2022CLTYP4//Ministero dell'Università e della Ricerca/ ; }, mesh = {Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Monte Carlo Method ; *Models, Statistical ; Regression Analysis ; *Microbiota ; Multivariate Analysis ; Metagenomics ; }, abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this paper introduces a novel mixture distribution for multivariate counts and a regression model built upon it. The flexibility and interpretability of the proposed distribution accommodate both negative and positive dependence among taxa and are accompanied by numerous theoretical properties, including explicit expressions for inter- and intraclass correlations, thereby providing a powerful tool for understanding complex microbiome interactions. Furthermore, the regression model based on this distribution facilitates the clear identification and interpretation of relationships between taxa and covariates by modeling the marginal mean of the multivariate response (i.e., taxa counts). Inference is performed using a tailored Hamiltonian Monte Carlo estimation method combined with a spike-and-slab variable selection procedure. Extensive simulation studies and an application to a human gut microbiome dataset highlight the proposed model's substantial improvements over competing models in terms of fit, interpretability, and predictive performance.}, } @article {pmid40772300, year = {2025}, author = {Li, S and Huang, W and Ma, B and Xia, L and Hu, H and Sun, Y and Ni, H and Yuan, MM and Zhou, J and Zhang, J and Liang, Y}, title = {Viral Diversity Mediates Carbon Allocation for Ecosystem Multifunctionality Across Biomes.}, journal = {Global change biology}, volume = {31}, number = {8}, pages = {e70412}, doi = {10.1111/gcb.70412}, pmid = {40772300}, issn = {1365-2486}, support = {42425703//National Natural Science Foundation of China/ ; 2024QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; YSBR-108//CAS (Chinese Academy of Sciences) Project for Young Scientists in Basic Research/ ; ISSASIP2201//Innovation Program of Institute of Soil Science/ ; 2022ZB467//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; }, mesh = {*Carbon/metabolism ; *Soil Microbiology ; *Ecosystem ; *Viruses/classification/genetics ; Metagenome ; Soil/chemistry ; Biodiversity ; }, abstract = {Viral diversity is essential for regulating the stability of ecosystem function by modulating the biochemical cycles via alterations in the survival and metabolic processes of host organisms. However, how viral survival strategies impact ecosystem function remains unresolved. Here, we analyzed 1824 metagenomes from soils across eight biomes, revealing that lytic viruses constituted a dominant proportion (88%) of the viral communities, with Siphoviridae (35.34%) being the most abundant lytic viral group. Viral communities significantly impacted soil organic carbon dynamics, while ecosystem multifunctionality was notably influenced by microbial necromass carbon, microbial biomass carbon, and various environmental factors. Microbial carbon use efficiency was the primary driver of ecosystem multifunctionality, with significant modulation by lytic and lysogenic viral communities, and lytic viruses contributed more directly to ecosystem multifunctionality (3%) compared to lysogenic viruses (1%). Our study underscores the pivotal role of viral communities, particularly lytic viruses, in shaping global carbon dynamics and ecosystem function, thereby providing a novel framework for future carbon management.}, } @article {pmid40770776, year = {2025}, author = {Kauer, L and Sapountzis, P and Imholt, C and Berens, C and Kuehn, R}, title = {Microbial exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {84}, pmid = {40770776}, issn = {2524-4671}, abstract = {The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.}, } @article {pmid40770684, year = {2025}, author = {Winand, R and D'hooge, E and Van Uffelen, A and Bogaerts, B and Van Braekel, J and Hoffman, S and Roosens, NHCJ and Becker, P and De Keersmaecker, SCJ and Vanneste, K}, title = {Investigating fungal diversity through metabarcoding for environmental samples: assessment of ITS1 and ITS2 Illumina sequencing using multiple defined mock communities with different classification methods and reference databases.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {729}, pmid = {40770684}, issn = {1471-2164}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *High-Throughput Nucleotide Sequencing ; *Biodiversity ; *DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Software ; Computational Biology/methods ; DNA, Fungal/genetics ; Sequence Analysis, DNA ; }, abstract = {An important challenge in taxonomic classification of environmental samples is capturing the real diversity by identifying all species present in a sample. Metabarcoding approaches are often employed to identify species in complex samples. The internal transcribed spacer (ITS) region is the official, widely adopted, barcode for identifying fungal species. Metabarcoding can be done in many different ways with multiple choices at different steps of the workflow. We present a comparative evaluation of the sequenced region (ITS1 and/or ITS2), two different reference databases (UNITE versus BCCM/IHEM), two different bioinformatics software packages (BLAST versus mothur), and the considered taxonomic level (species versus genus level), to accurately capture the diversity using 37 fungal defined mock communities (DMCs). The DMCs cover a broad range of fungal diversity, including 42 Ascomycota species (26 genera), 4 Basidiomycota species (4 genera), and 5 Mucoromycota species (5 genera), all commonly found in indoor environments in Western Europe. Classification performance was first evaluated using ITS1 and ITS2 sequences of all species in the DMCs, generated by Sanger sequencing, to evaluate the discriminatory power of ITS and set a baseline for subsequent comparison with Illumina sequencing. Classification performance was found to be variable depending on all considered variables (sequencing technology, taxonomic level, ITS region, software, database) with 56-100% of species correctly assigned. Sanger sequencing showed that neither ITS1 nor ITS2 resulted in optimal performance due to its low discriminatory power within certain genera. Compared to Sanger sequencing, Illumina sequencing generally resulted in lower precision but comparable recall. Classification performance was generally good at genus but not at species level, although intermediate taxonomic levels could present adequate alternatives. ITS2 typically resulted in slightly better precision and comparable recall compared to ITS1. The employed reference database had a marked effect, with BCCM/IHEM performing better than UNITE due to the difference in number of sequences in each database. BLAST resulted in better performance, but required expert curation, whereas mothur performed better when using an automated workflow. Estimating species abundances using Illumina sequencing read counts generally performed only poorly, although read abundance filtering could increase the precision of ITS1, but not ITS2. Each approach comes with its own advantages and inconveniences and should be carefully selected based on the objectives of the analysis. Our results highlight the power of metabarcoding using Illumina sequencing for investigating fungal diversity in complex samples and can guide scientists in selecting the most appropriate setup for their own purposes.}, } @article {pmid40770608, year = {2025}, author = {Babalola, OO and Shittu, OE and Enagbonma, BJ}, title = {Unveiling the Allium ampeloprasum rhizosphere microbiome and its functional dataset under different fertilization systems.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {54}, pmid = {40770608}, issn = {2730-6844}, support = {CRP/ZAF22-03//NRF, South Africa and ICGEB, Italy/ ; }, mesh = {*Rhizosphere ; *Allium/microbiology ; *Microbiota ; Metagenomics ; Fertilizers ; Soil Microbiology ; Bacteria/genetics/classification ; }, abstract = {Leek (Allium ampeloprasum) is a nutritious vegetable popularly cultivated in South Africa and most regions of the world. It is generally recognised as a source of vitamins and vegetables. Nevertheless, little is known about its rhizosphere microbiome and its microbial functional dataset under various fertilization systems. Therefore, this study intended to unveil the rhizosphere microbiome of Allium ampeloprasum and their functional datasets through shotgun metagenomics sequencing analysis.}, } @article {pmid40770383, year = {2025}, author = {Zhou, Z and Niu, Y and Ma, Y and Zhang, D and Wang, Y and Ji, R and Zhao, J and Ma, C and Zhu, H and Liu, Y and Tu, L and Lu, J and Zhang, B and Zhang, H and Ma, X and Chen, P}, title = {Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {181}, pmid = {40770383}, issn = {2049-2618}, support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//The Lanzhou Municipal Science and Technology Program/ ; 20250260006//the College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; }, mesh = {*Fusobacterium nucleatum/drug effects ; Animals ; Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology/drug therapy ; Mice ; Feces/microbiology ; *Fusobacterium Infections/microbiology ; Bifidobacterium/genetics ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Male ; Amidohydrolases/metabolism/genetics ; Bile Acids and Salts/metabolism ; Female ; Cell Proliferation ; Escherichia coli/genetics ; Cell Line, Tumor ; Disease Models, Animal ; }, abstract = {BACKGROUND: Fusobacterium nucleatum (F. nucleatum) is prevalent in colorectal cancer (CRC), and it can promote proliferation and induce chemoresistance via multiple pathways. The development of treatment strategies for F. nucleatum-infected CRC is of great importance.

METHODS: Shotgun metagenomic and metabolomic analyses of human feces, as well as metabolomic analysis of human blood, were performed to reveal the dysbiosis and metabolic dysregulation in CRC. Furthermore, the effects of Bifidobacterium animalis (B. animalis) on F. nucleatum and CRC were assessed in vitro and in vivo. Using a mouse CRC model, the function of bile salt hydrolase (BSH) in B. animalis was verified through heterologous expression in Escherichia coli (E. coli). Bile acids and drug library screening experiments were performed to inhibit F. nucleatum and tumor proliferation.

RESULTS: We identified an increase in F. nucleatum, enrichment of lipid metabolites, and depletion of Bifidobacterium in CRC patients. Furthermore, B. animalis inhibited F. nucleatum and CRC cells growth in an acid-dependent manner and reduced F. nucleatum-induced tumor increasement in mice. Mechanistically, F. nucleatum caused lipid accumulation, exacerbated inflammation, and intestinal barrier disruption, whereas B. animalis alleviated these changes, increased the Simpson diversity index, reduced lipid metabolites, and altered secondary bile acid composition in mice. Moreover, E. coli-BSH and ursodeoxycholic acid (UDCA) inhibited F. nucleatum-induced lipid accumulation and FASN/CPT1/NF-κB upregulation. Additionally, they alleviated F. nucleatum-related intestinal tumorigenesis in vivo. Targeting F. nucleatum-infected CRC cells and subcutaneous tumors in mice, penfluridol or the combination of orlistat and 5-FU exhibited superior inhibitory effects compared to 5-FU alone.

CONCLUSIONS: F. nucleatum and lipid metabolites are enriched in CRC patients. Furthermore, BSH-expressing E. coli, UDCA, and penfluridol can alleviate F. nucleatum-induced lipid accumulation and tumor growth in mice. Video Abstract.}, } @article {pmid40769940, year = {2025}, author = {De Corte, D and Dlugosch, L and Srivastava, A and Simon, M and Hansell, DA and Bercovici, S and Orellana, M}, title = {Taxonomic and Functional Features of Surface to Deep-Sea Prokaryotic Communities in the Eastern North Pacific Ocean.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70170}, pmid = {40769940}, issn = {1758-2229}, support = {CO 2218/2-1//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; OCE-1634009//National Science Foundation/ ; OCE-1634250//National Science Foundation/ ; }, mesh = {Pacific Ocean ; *Seawater/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Archaea/classification/genetics/isolation & purification/metabolism ; Phylogeny ; *Microbiota ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; }, abstract = {Biogeochemical cycles in the ocean are strongly influenced by microbial activity, which affects nutrient and organic matter cycling. These processes, influenced by factors such as temperature, salinity, density and inorganic nutrients, drive the vertical stratification of microbial communities, which subsequently influence the chemistry at different depth layers. Sequencing technology has expanded our understanding of oceanic prokaryotic communities' taxonomic and functional potential. However, there is limited information on how these communities vary across gradients. In this study, we conducted metagenomic analyses on samples from the eastern North Pacific, collected across a longitudinal transect around 45°N and throughout the entire water column. We assessed taxonomic and functional classification, focusing on the roles of prokaryotic communities in biogeochemical cycling. Our results revealed that the surface community was dominated by the SAR11 clade, followed by Flavobacterales and Rhodobacterales. The deep layers harboured a more diverse community, where Thaumarchaeota accounted for the most significant proportion. This clear taxonomic stratification led to variations in the communities' functional capabilities across different depth layers. Photosynthesis and heterotrophy dominated the surface layers, whereas the deeper layers exhibited a mix of metabolic features, allowing organisms to potentially utilise both inorganic and organic carbon sources.}, } @article {pmid40767981, year = {2025}, author = {Jena, R and Singh, NA and Ahmed, N and Choudhury, PK}, title = {Bifidobacteria in antibiotic-associated dysbiosis: restoring balance in the gut microbiome.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {8}, pages = {297}, pmid = {40767981}, issn = {1573-0972}, mesh = {*Dysbiosis/chemically induced/microbiology/therapy ; Humans ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium/physiology ; *Anti-Bacterial Agents/adverse effects ; Animals ; Prebiotics ; }, abstract = {Antibiotic-associated dysbiosis disrupts the gut's microbial balance, leading to reduced diversity, overgrowth of antibiotic-resistant strains, and compromised gut homeostasis. This can result in inflammation, increased intestinal permeability, impaired immunity, and heightened susceptibility to infections. In this context, probiotics have been highlighted as a promising remedy in alleviating this antibiotic-induced gut microbiome aberrations with subsequent decrease of the detrimental effects. Bifidobacteria, a prominent bacterial group with promising probiotic attributes, have shown effectiveness in restoring the gut microbiome by strong adherence to the colon's mucosal lining and enhancing the immune response through increased anti-inflammatory cytokines. They also play a crucial role as key producers of acetic acid, which supports butyric acid-producing bacteria essential for colonocyte health during dysbiosis. The synergistic use of bifidobacteria with other probiotic species or prebiotic substrates has further enhanced their survival, colonization capacity, and overall impact on gut microbial restoration. Advanced metagenomic analyses have begun to reveal strain-specific functions, paving the way for personalized probiotic therapies tailored to an individual's unique microbiome profile. Despite encouraging progress, critical research gaps persist, particularly regarding strain-specific efficacy, formulation stability, long-term outcomes, underlying mechanisms, systemic interactions, and the distinct and specific role of bifidobacteria. Addressing these gaps through targeted clinical investigations is essential to fully harness their therapeutic potential and develop optimized strategies for restoring the microbial balance in the gut microbiome.}, } @article {pmid40766845, year = {2025}, author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS}, title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1562965}, pmid = {40766845}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation & purification ; *Virus Diseases/virology ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.

METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.

RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.

CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.}, } @article {pmid40764903, year = {2025}, author = {Jingwen, J and Jingran, F and Liye, M and Yu, H and Yancen, M and Jingya, Z}, title = {The role of cervical microbiome in cervical incompetence: insights from 16 S rRNA metagenomic sequencing.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {486}, pmid = {40764903}, issn = {1471-2180}, support = {No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; }, mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pregnancy ; Metagenomics ; Adult ; *Uterine Cervical Incompetence/microbiology/immunology ; *Bacteria/classification/genetics/isolation & purification ; *Cervix Uteri/microbiology ; NF-kappa B/metabolism ; Toll-Like Receptor 2/metabolism/genetics ; Toll-Like Receptor 4/metabolism/genetics ; Cervix Mucus/microbiology ; }, abstract = {Cervical incompetence (CI) is recognized as a critical factor contributing to mid-pregnancy miscarriage and preterm delivery, significantly affecting pregnancy outcomes. Despite this, the specific role of the microbiome in this pathological process remains inadequately understood. This study seeks to elucidate the core microbiome associated with CI in pregnant women and explore its potential biological mechanisms. Utilizing 16 S rRNA metagenomic sequencing, we examined the cervical mucus microbiota of women with CI both pre-operatively (PreOp) and post-operatively (PostOp). Subsequently, the immunomodulatory effects of these microbial communities on the immune system were systematically assessed using quantitative real-time PCR, Western blotting, and enzyme-linked immunosorbent assay. The findings revealed a significant reduction in microbial diversity and richness in PostOp cervical mucus, alongside notable alterations in microbiota composition. The genera Lactobacillus, Bifidobacterium, Gardnerella, Streptococcus, and Anaerococcus were identified as predominant. Further analysis demonstrated that treatment with 25% Lactobacillus crispatus (L. crispatus) supernatants, in comparison to 25% Group B Streptococcus (GBS) supernatants, resulted in high cell viability and normal morphology in HcerEpic cells. Importantly, the combination of 25% L. crispatus and 25% GBS supernatants significantly reduced the mRNA and protein expression levels of Toll-like receptor 4 (TLR4), Toll-like receptor 2 (TLR2), and nuclear factor kappa B (NF-κB) in vitro. These results indicate that L. crispatus may play a role in modulating cervical inflammation in CI by suppressing the TLR/NF-κB signaling pathway, potentially contributing to a more stable cervical microenvironment during pregnancy.}, } @article {pmid40761666, year = {2025}, author = {Zhou, H and Mu, X and Hu, H and Zhao, S and Hu, N and Yang, M and Jiang, J}, title = {DHLCA Alleviates Diabetic Kidney Disease via TGR5/FXR Activation and Gut Microbiota Remodeling.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {6469-6485}, pmid = {40761666}, issn = {1177-8881}, mesh = {*Receptors, G-Protein-Coupled/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Diabetic Nephropathies/drug therapy/metabolism ; Animals ; Mice ; Male ; Humans ; *Receptors, Cytoplasmic and Nuclear/metabolism/agonists ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; Middle Aged ; Diabetes Mellitus, Experimental/drug therapy/metabolism ; Mice, Inbred C57BL ; Female ; *Lithocholic Acid/analogs & derivatives/pharmacology ; Disease Models, Animal ; }, abstract = {PURPOSE: Diabetic kidney disease (DKD) is a major contributor to chronic kidney disease worldwide. Bile acids (BAs) are increasingly recognized as key regulators of glucose metabolism and kidney function. This study aimed to investigate the role of BA metabolism in the progression of DKD.

METHODS: Plasma BA profiles were measured in healthy controls (HC), patients with type 2 diabetes mellitus (T2DM), and patients with DKD using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). After identifying potential BA biomarkers in the clinical cohort, in vivo validation was conducted using dehydrolithocholic acid (DHLCA) intervention in DKD mouse model. Kidney injury markers, as well as the expression of Takeda G protein-coupled receptor 5 (TGR5) and farnesoid X receptor (FXR), were evaluated. In addition, gut microbiota (GM) composition was analyzed via metagenomic sequencing following DHLCA treatment.

RESULTS: The plasma DHLCA levels were significantly lower in DKD with macroalbuminuria group compared to T2DM group and DKD with microalbuminuria group (P < 0.01). Partial Spearman correlation analysis adjusted for age and diabetes duration showed that DHLCA levels were negatively correlated with urine albumin (ρ = -0.347; 95% CI, -0.531 to -0.135; q = 0.008) and urine albumin-to-creatinine ratio (UACR) (ρ = -0.332; 95% CI, -0.499 to -0.155; q = 0.010). In vivo, DHLCA administration significantly reduced UACR and fasting blood glucose (FBG) levels (P < 0.01), and improved liver function (ALT, P < 0.05) in DKD mice. DHLCA treatment attenuated renal tubular injury, restored TGR5 and FXR expression in kidney tissue, and decreased levels of kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL). Metagenomic analysis revealed an enrichment of Lachnospiraceae bacterium following DHLCA treatment.

CONCLUSION: DHLCA may represent a promising therapeutic candidate for DKD by targeting the TGR5/FXR signaling pathway and GM remodeling. Its metabolic and kidney benefits, along with an improved hepatic profile and absence of hepatotoxicity, support further translational investigation.}, } @article {pmid40757481, year = {2025}, author = {Bustos-Caparros, E and Viver, T and Gago, JF and Avontuur, JR and Amiour, S and Baxter, BK and Llames, ME and Mutlu, MB and Oren, A and Ramírez, AS and Stott, MB and Venter, SN and Santos, F and Antón, J and Rodriguez-R, LM and Bosch, R and Hedlund, BP and Konstantinidis, KT and Rossello-Mora, R}, title = {Global dominance of Haloquadratum walsbyi by a single highly clonal genomovar with distinct gene content and viral cohorts from close relatives.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf165}, pmid = {40757481}, issn = {1751-7370}, abstract = {Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > ANI > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.}, } @article {pmid40755755, year = {2025}, author = {Vicente-Valor, J and Tesolato, S and Gómez-Garre, D and Paz-Cabezas, M and Ortega-Hernández, A and Fernández-Hernández, C and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Rupérez, FJ and García, A and Torres, A and Iniesta, P}, title = {Identification of clinically relevant profiles in colorectal cancer through integrated analysis of bacterial DNA and metabolome in serum.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1562416}, pmid = {40755755}, issn = {1664-3224}, mesh = {Humans ; *Colorectal Neoplasms/blood/diagnosis/microbiology/metabolism ; Male ; Female ; Middle Aged ; *Metabolome ; *DNA, Bacterial/blood/genetics ; Aged ; Cross-Sectional Studies ; *Biomarkers, Tumor/blood ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome ; Metabolomics/methods ; Adult ; Bacteria/genetics ; }, abstract = {INTRODUCTION: There is increasing evidence demonstrating the relationship between microbiota and colorectal cancer. Several studies have been published analyzing microbiota in tissues and feces from cancer patients; however, there are only a few publications investigating the clinical utility of serum microbiome from colorectal cancer patients. Our aim was to advance in the search for serum biomarkers for the diagnosis of colorectal cancer.

METHODS: We conducted a cross-sectional study assessing bacterial DNA and metabolomic profiles in 64 serum samples from subjects affected by colorectal cancer and controls. A metagenomic analysis of the bacterial 16S rRNA gene in serum was established, and serum metabolites were detected through an untargeted metabolic study based on Gas Chromatography-Quadruple Time-Of-Flight Mass Spectrometry with accurate mass.

RESULTS AND DISCUSSION: After integrating the data resulting from the bioinformatics and statistical analyses, we obtained different profiles in colorectal cancer population and controls, regardless of the subjects' age, gender and body mass index. Serum levels of Firmicutes and threonic acid were the most relevant characteristics that could help differentiate both groups, achieving an excellent predictive accuracy in this discovery cohort (area under the ROC curve = 0.95). Although these results should be validated in other cohorts through multicenter studies, we consider that our data could be relevant and applicable to the early diagnosis of colorectal cancer.}, } @article {pmid40755247, year = {2025}, author = {Nadimpalli, ML and Sehgal, N and Rojas-Salvatierra, L and Gilman, RH and Earl, AM and Worby, CJ and Schwab, M and Pickering, AJ and Pajuelo, MJ}, title = {Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2541029}, pmid = {40755247}, issn = {1949-0984}, support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; R01 AI108695/AI/NIAID NIH HHS/United States ; T32 ES012870/ES/NIEHS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Peru/epidemiology ; *beta-Lactamases/metabolism/genetics ; Infant ; Feces/microbiology ; Male ; *Enterobacteriaceae/genetics/enzymology/isolation & purification/classification ; Female ; Child, Preschool ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Metagenomics ; }, abstract = {Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low- and middle-income countries. Some children nevertheless remain never or rarely colonized during early life. Understanding how this protection is conferred could be helpful for designing future interventions to protect children's health. Here, we investigated whether differences in gut microbiome development could underlie differential susceptibility to ESBL-E gut colonization over time among children in peri-urban Lima. Weekly stool and daily surveys were collected from 345 children < 3 years old during a 2016-19 study of enteric infections. A subset of children (n = 12) was rarely gut-colonized with ESBL-E from 1-16 months of age. We performed short-read metagenomic sequencing of stool collected at 3, 6, 7, 9, 12, and 16 months from these children and a random subset of 42 frequently colonized children, and characterized differences in their exposures and gut microbiomes. No differences in gut taxa or functional pathways were identified over time, though children harbored differentially abundant taxa, more unique E. coli strains, and a higher abundance of blaCTX-M gene copies at ESBL-E-positive versus negative timepoints. Differing patterns of ESBL-E colonization over time among children in peri-urban Lima do not appear to be related to differences in gut microbiome development.}, } @article {pmid40755225, year = {2025}, author = {Pan, Z and Walsh, CJ and Feehily, C and Nori, SRC and McAuliffe, FM and Cotter, PD and MacSharry, J and van Sinderen, D}, title = {Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2541033}, pmid = {40755225}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Breast Feeding ; *Milk, Human/microbiology ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; }, abstract = {The infant resistome, the collection of antimicrobial resistance genes (ARGs) of newborns, is critical for gut microbiota establishment. Using metagenomic sequencing data, we analyzed various 1-week and 1-month postpartum samples to study infant resistome establishment, ARG transmission, and its impact on functional redundancy of the microbiota. A total of 431 samples were analyzed; infant stools (1-week, n = 119; 1-month, n = 119), maternal stools (1-month postpartum, n = 120), and breastmilk (1-month postpartum, n = 73). Breastfeeding correlated with increased functional redundancy and altered bacterial-ARG co-occurrence networks in the infant resistome. Escherichia coli dominated early resistome dynamics with a higher abundance correlating with reduced functional redundancy. Bifidobacterium longum exhibited a consistent negative association with 21 ARGs at one-month in breastfed infants, while four negative relationships between ARGs and Bifidobacterium bifidum were observed in formula-fed infants. ARG transmission via breastmilk appears to be gene-specific, with the quinolone resistance gene sdrM likely transmitted under maternal antibiotic use. Delivery mode modulated the microbial environment in ways that interact with resistome structure and changing functional redundancy, particularly through genera like Staphylococcus and Streptococcus. These findings highlight the role of early feeding practices in resistome development and propose functional redundancy as a key ecological framework for understanding infant gut resistome dynamics.}, } @article {pmid40753386, year = {2025}, author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O}, title = {The effects of dietary fat on gut microbial composition and function in a mouse model of ovarian cancer.}, journal = {Journal of ovarian research}, volume = {18}, number = {1}, pages = {174}, pmid = {40753386}, issn = {1757-2215}, support = {K12 CA076917/CA/NCI NIH HHS/United States ; K12CA076917//NIH K12CA076917 Clinical Oncology Training Program/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; *Ovarian Neoplasms/microbiology/pathology ; Mice ; Disease Models, Animal ; Humans ; *Dietary Fats/pharmacology ; Diet, Ketogenic ; Cell Line, Tumor ; Mice, Inbred C57BL ; Diet, High-Fat ; }, abstract = {OBJECTIVES: The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC).

METHODS: Thirty female C57BL/6 J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function.

RESULTS: Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides, Lachnospiracae bacterium, Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides. Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice.

CONCLUSIONS: These results highlight the intricate relationship between diet andthe gut microbiome in promoting EOC growth. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.}, } @article {pmid40753152, year = {2025}, author = {Jiang, W and Li, Y and Yang, J and Tan, X and Tian, R and Ma, G and Wu, J and Zhang, J and Huang, Y and Liu, P and Yuan, M and Song, X and Luo, L and Zhou, X and Zuo, H and Wong, ML and Licino, J and Zheng, P}, title = {Chronic stress in mice: how gut bacteria influence gene activity in key brain neurons.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {262}, pmid = {40753152}, issn = {2158-3188}, support = {2024MD754023//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; Mice ; *Stress, Psychological/microbiology/metabolism/genetics ; *Neurons/metabolism ; *Hypothalamus/metabolism ; Male ; Disease Models, Animal ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; *Depressive Disorder, Major/microbiology ; Mice, Inbred C57BL ; }, abstract = {Major depressive disorder (MDD) is a serious mental disorder. Increasing evidence suggests that changes of gut microbiota are involved in pathogenesis of depression, yet the underlying mechanisms remains unknown. Here, chronic unpredictable mild stress (CUMS) mice model was constructed to mimic depression. We characterized the microbial composition and function of control, bedding exchange, and CUMS mice through 16S rRNA gene and metagenomic sequencing. Additionally, single-nucleus RNA sequencing (snRNA-seq) was used to compare the transcriptomic changes in the hypothalamus of these three groups. We found that replacing the bedding of CUMS mice with that of control mice could reverse the depressive-like behaviors. The microbial signatures of bedding exchange group trended towards the control group at the genus level. The abundance of g_norank_f_Muribaculaceae significantly increased in the bedding exchange group compared to CUMS group. Meanwhile, we found that the CUMS mice were characterized by cell-specific transcriptomic changes in hypothalamus. Notably, the transcriptomes of excitatory neurons in the hypothalamus were mainly affected, and these changes could be effectively reversed by bedding exchange treatment. The gene modules analysis revealed that the gut microbiota mainly modulated glyoxylate and dicarboxylate metabolism as well as arginine biosynthesis in hypothalamic excitatory neurons. Our findings provide new insights into the pathogenesis of depression.}, } @article {pmid40751224, year = {2025}, author = {Reinoso-Peláez, EL and Saura, M and González, C and Ramón, M and Calvo, JH and Serrano, M}, title = {The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {177}, pmid = {40751224}, issn = {2049-2618}, support = {RTI-2018-096487-R-C33//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Female ; Animals ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Sheep/microbiology ; *Fertility ; *Bacteria/classification/genetics/isolation & purification ; Pregnancy ; Genomics ; Metagenome ; }, abstract = {BACKGROUND: Despite advancements in artificial insemination, sheep fertility rates remain suboptimal. Recent studies in other species highlight the critical role of reproductive microbiota in influencing fertility outcomes. This research explores the relationship between ovine vaginal microbiota, associated functional pathways, and fertility using advanced nanopore long-reading metagenomic sequencing on 297 ewes from three Spanish breeds across four herds. The study aimed to describe a core vaginal microbiota, analyse the complex interactions with herd, breed, age, and parity factors, and identify taxa and genes associated with reproductive success by artificial insemination.

RESULTS: The study identified Staphylococcus, Escherichia, and Histophilus as the most abundant genera. Microbial communities varied considerably between breeds and herds, with high predictive accuracy (> 90%) in classification models. Differential abundance analysis revealed that the genera Histophilus, Fusobacterium, Bacteroides, Campylobacter, Streptobacillus, Gemella, Peptoniphilus, Helococcus, Treponema, Tissierella, and Phocaeicola were more abundant in non-pregnant ewes. Some of these taxa were also associated with four COG entries and one KEGG orthologue significantly linked to non-pregnancy, primarily involving carbohydrate metabolism, defence mechanisms, and structural resilience. Age and parity were also associated with microbiota composition, particularly in ewes older than five years or with more than three parturitions, suggesting that cumulative physiological changes may contribute to microbial shifts over time.

CONCLUSIONS: The ewe's vaginal microbiome appears to be mainly influenced by both herd and breed, though distinguishing genetic from environmental factors is challenging within our study design. While the overall microbiota showed a subtle effect on pregnancy, certain genera had a significant negative impact, likely due to pathogenic or inflammatory properties that disrupt reproductive health. The metagenomic approach used here enabled not only comprehensive taxonomic classification but also detailed functional analysis, providing deeper insights into the microbiome's role in reproductive outcomes. Video Abstract.}, } @article {pmid40750823, year = {2025}, author = {Adebayo, AA and Enagbonma, BJ and Babalola, OO}, title = {Comparative metagenomics on community structure and diversity of rhizomicrobiome associated with monoculture and soybean precedent carrot.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {28161}, pmid = {40750823}, issn = {2045-2322}, mesh = {*Daucus carota/microbiology/growth & development ; *Glycine max/microbiology/growth & development ; Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Plant Roots/microbiology ; Biodiversity ; Agriculture/methods ; }, abstract = {Several studies have explored the impact of cropping systems, including monoculture and crop rotation, on the plant rhizosphere - an essential dynamic in designing strategies for optimizing soil health and crop productivity. It remains largely unknown how these agricultural practices drive the diversity and community structure of the microbiome in the carrot rhizosphere. Thus, this study aims to profile the core rhizo-microbiome of carrots grown under a monoculture system and those grown after soybean cultivation. The microbial DNA extracted from 12 soil samples collected from monoculture carrot rhizosphere (MCR), soybean-precedent carrot rhizosphere (SCR), and uncultivated land (bulk soils) (BS) were analyzed via shotgun metagenomics sequencing. Findings show that bacterial phyla were the most dominant taxa across the sampling points. Principal Component Analysis (PCA) revealed that Pseudomonadota, Bacillota, and Actinomycetota are significantly enriched in soybean-precedent carrot rhizosphere, monoculture carrot rhizosphere, and bulk soil, respectively. Furthermore, genera Bradyrhizobium and Agromyces were significantly enriched, and Rhodococcus was exclusively present in soybean-precedent carrot rhizosphere. Alpha and Beta diversity analyses indicated that the microbial community composition was unique within and between the sampling sites (genus level). Redundancy Analysis (RDA) demonstrated that soil properties like silt (contributing 84.2%), total nitrogen (contributing 83.2%), organic carbon (contributing 81.0%), and sand texture (contributing 75.8%) explained the variance in microbiome composition. This study provides fundamental insight into how cropping systems influence carrot rhizo-microbiome. Crop rotation practice with soybeans was found to increase microbial composition and diversity in carrot plantations.}, } @article {pmid40748897, year = {2025}, author = {Ségurel, L and Ulaganathan, TS and Mathieu, S and Loiodice, M and Poulet, L and Drouillard, S and Cygler, M and Helbert, W}, title = {The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations.}, journal = {PloS one}, volume = {20}, number = {8}, pages = {e0329457}, pmid = {40748897}, issn = {1932-6203}, mesh = {Humans ; Asia, Eastern/ethnology ; Bacterial Proteins/genetics/metabolism ; *Bacteroides/enzymology/genetics ; *East Asian People/statistics & numerical data ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Glycoside Hydrolases/genetics/metabolism ; Metagenome ; Phylogeny ; *Polysaccharides, Bacterial/metabolism ; *Porphyra/microbiology ; Sepharose/analogs & derivatives ; }, abstract = {The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. An illustrative example of that is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates as well as metagenomic data from more than 14,000 worldwide individuals, we found that the porphyran PUL is present in 17 different Phocaeicola/Bacteroides species (including 12 species that were not known to carry it), as well as in two Parabacteroides species and two genera from the Bacillota phylum, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the prevalence of this porphyran PUL across 32 countries and showed that it exists in appreciable frequencies (>1%) only in East Asia (Japan, China, Korea). Finally, we identified three major PUL haplotypes which frequencies significantly differ between these East Asian countries. This geographic structure likely reflects the rate of bacterial horizontal transmission between individuals.}, } @article {pmid40748490, year = {2025}, author = {He, T and Wang, Y and Zhao, L and Che, Y and Zhang, L and Zeng, Y and Shen, H and Hao, H and Cao, L}, title = {Integrated Microbiota-Bile Acid Analysis as Potential NonInvasive Biomarkers for Ulcerative Colitis Staging Diagnose.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {15}, pages = {e70859}, doi = {10.1096/fj.202501078R}, pmid = {40748490}, issn = {1530-6860}, support = {2021YFA1301300//the National Key Research and Development Program of China/ ; 2022YFF1100601//the National Key Research and Development Program of China/ ; 82173886//the National Natural Science Foundation of China/ ; 82373886//the National Natural Science Foundation of China/ ; 82404997//the National Natural Science Foundation of China/ ; G20582017001//111 Plan | Overseas Expertise Introduction Project for Discipline Innovation/ ; SKLNMZZ202402//the Project of State Key Laboratory of Natural Medicines, China Pharmaceutical University/ ; }, mesh = {Humans ; *Colitis, Ulcerative/diagnosis/microbiology/metabolism/blood ; *Bile Acids and Salts/metabolism/blood/analysis ; Male ; Biomarkers/metabolism/blood ; Adult ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Clinical staging diagnosis and progression tracking for ulcerative colitis (UC) is as challenging as poor patient compliance with endoscopic biopsy. We perform a study that integrates metabolomic profiling, 16S rRNA, and metagenomic sequencing on serum and fecal samples from 23 active state UC patients, 24 remission state UC patients, and 20 healthy volunteers from China, aiming to explore a non-invasive integrative biochemical index to quantitatively track and monitor pathological activity of UC. Besides the known associations of microbes such as Fusobacterium nucleatum and Clostridium symbiosum with UC, we found several bile acid-transforming species, including 7α-dehydroxygenase and 7α/β-dehydrogenase expressing microbiota, were significantly correlated with UC pathological activity. We identified 2 bacterial gene markers related to secondary bile acid synthesis besides Clostridium scindens that differentiated active and remission stage UC and healthy control microbiomes. Relevantly, reduced serum deoxycholic acid (DCA)/cholic acid (CA) species ratio and increased fecal ursodeoxycholic acid (UDCA)/chenodeoxycholic acid (CDCA) ratio were associated with the pathological activity of UC. Moreover, receiver operating characteristic analysis based on serum/fecal bile acid ratios was much more accurate in the prediction of active and remission stage outcomes. This species-specific temporal change and bile acid dysregulation pattern linked to disease severity indicate that integrated microbiome-bile acid profiles may be implied for disease activity prediction and that targeting microbiome-mediated gut flora and bile acid homeostasis may be implicative of therapy efficacy. These insights will help improve clinical diagnosis and optimize existing medical treatments.}, } @article {pmid40746878, year = {2025}, author = {Xu, F and Li, W and Zheng, XJ and Hao, Y and Yang, YH and Yang, H and Zhang, S and Cao, WX and Li, XX and Zhang, X and Du, GH and Ji, TF and Wang, JH}, title = {3-O-Acetyl-11-Keto-β-Boswellic Acid Suppresses Colitis-Associated Colorectal Cancer by Inhibiting the NF-Kb Signaling Pathway and Remodeling Gut Microbiota.}, journal = {Oncology research}, volume = {33}, number = {8}, pages = {1969-1989}, pmid = {40746878}, issn = {1555-3906}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Humans ; *Triterpenes/pharmacology ; *NF-kappa B/metabolism ; Signal Transduction/drug effects ; *Colitis-Associated Neoplasms/drug therapy/pathology/metabolism/microbiology ; Cell Proliferation/drug effects ; Apoptosis/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Colitis/complications/drug therapy ; Disease Models, Animal ; Cell Line, Tumor ; Male ; HCT116 Cells ; }, abstract = {OBJECTIVES: Colorectal cancer (CRC) is one of the most common cancers all over the world. The progression of CRC is associated with inflammation and disruptions in intestinal flora. 3-O-Acetyl-11-keto-β-boswellic acid (AKBA) has been noted for its potent anti-inflammatory properties. However, the effect of AKBA on colon cancer caused by inflammation and its mechanism are not unclear. The study is to explore the effect of AKBA on CRC and its mechanism.

MATERIALS AND METHODS: Cell proliferation, (5-ethynyl-2[']-deoxyuridine, EdU)-DNA synthesis assay and colony formation were used to assess the effect of AKBA on the proliferation of CRC cells. Flow cytometry was employed to analyze the cell cycle and apoptosis rate of cells treated with AKBA. RNA sequencing was done to explore the underlying mechanisms of AKBA. Western blot was used to assess the expression of key proteins in the nuclear factor kappa-B (NF-κB) signaling pathway after the treatment of AKBA. Real-time quantitative PCR (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), and Meso Scale Discovery (MSD) assays were employed to check the anti-inflammation effects of AKBA on Lipopolysaccharide (LPS)-induced RAW264.7 cells and LPS-induced mouse model. Additionally, the Azoxymethane/Dextran sulfate sodium (AOM/DSS)-induced colitis-associated CRC model was used to evaluate the anti-CRC effect of AKBA. Gut microbiota profiling of fecal samples from CRC mice, both with and without AKBA treatment, was conducted through metagenomic sequencing analysis.

RESULTS: Our results showed that AKBA reduced the proliferation of HCT116 and SW620 cells, increased apoptosis of cells, and arrested the cell cycle at the G2/M phase. Results from RNA-seq showed that AKBA inhibited CRC by inhibiting the NF-κB signaling pathway and reducing cellular inflammation. Furthermore, AKBA reduced the levels of inflammatory cytokines, including tumor necrosis factor-α (TNF-α), Interferon-γ (IFN-γ), Interleukin-IL-12p70 (IL-12p70), Interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) in both the spleen and serum of LPS-induced acute inflammation mice. Additionally, AKBA inhibited the development of AOM/DSS-induced colitis-associated colon cancer in mice and positively influenced gut microbiota.

CONCLUSION: This study highlights the inhibitory effect of AKBA on colitis-associated CRC and reveals a novel aspect of its role in the remodeling of gut microbiota. These findings suggest that AKBA may be used as a potential therapeutic agent for CRC.}, } @article {pmid40745465, year = {2025}, author = {Popova, A and Rācenis, K and Brīvība, M and Saksis, R and Saulīte, M and Šlisere, B and Berga-Švītiņa, E and Oļeiņika, K and Saulīte, AJ and Seilis, J and Kroiča, J and Čerņevskis, H and Pētersons, A and Kloviņš, J and Lejnieks, A and Kuzema, V}, title = {Reduced butyrate-producing bacteria and altered metabolic pathways in the gut microbiome of immunoglobulin A nephropathy patients.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {28011}, pmid = {40745465}, issn = {2045-2322}, support = {lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; }, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/metabolism/pathology ; Female ; *Butyrates/metabolism ; Male ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; *Metabolic Networks and Pathways ; Cross-Sectional Studies ; Feces/microbiology ; *Bacteria/metabolism/genetics/classification ; Prospective Studies ; Immunoglobulin A/metabolism ; Case-Control Studies ; }, abstract = {Gut-associated lymphoid tissue is central to the production of galactose-deficient IgA1 (Gd-IgA1), a key factor in immunoglobulin A nephropathy (IgAN). Although no major differences in gut microbiome diversity have been reported across IgAN cohorts, functional alterations in microbial composition may contribute to disease pathogenesis. The study was designed as a cross-sectional study with an embedded prospective cohort component. Forty-eight adults with biopsy-confirmed IgAN-categorized as progressors (eGFR decline > 5 ml/min/1.73 m[2]/year, n = 23) or nonprogressors (n = 23)-and 23 healthy controls (HC) were recruited. Stool samples underwent metagenomic and functional profiling. Alpha diversity did not differ significantly between IgAN patients and HC. However, butyrate-producing bacteria (Butyrococcus, Agathobacter rectalis) were less abundant in IgAN patients. The sulfoquinovose degradation I pathway, associated with these bacteria, was also reduced. Nucleotide- and nucleoside-biosynthesis pathways were elevated in IgAN. Gd-IgA1 levels correlated with variations in metabolic pathways. Progressors demonstrated enhanced activity in isopropanol biosynthesis, biotin biosynthesis II, and phospholipid biosynthesis pathways. IgAN patients show reduced butyrate-producing bacteria and distinct functional changes in the gut microbiome suggestive of immune activation and inflammation. Progressors exhibit additional metabolic shifts linked to bacterial membrane stabilization.}, } @article {pmid40744923, year = {2025}, author = {Grossegesse, M and Horn, F and Kurth, A and Lasch, P and Nitsche, A and Doellinger, J}, title = {vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7041}, pmid = {40744923}, issn = {2041-1723}, mesh = {Humans ; *Proteomics/methods ; *SARS-CoV-2/isolation & purification/genetics ; *COVID-19/virology/diagnosis ; *Viruses/genetics/isolation & purification/classification ; Viral Proteins/metabolism ; Workflow ; *Virus Diseases/virology/diagnosis ; Genome, Viral ; Algorithms ; Peptide Library ; Virome ; Sensitivity and Specificity ; Metagenomics/methods ; Nasopharynx/virology ; }, abstract = {Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, we introduce proteomics as a complementary approach for the untargeted identification of human-pathogenic viruses from patient samples. The viral proteomics workflow (vPro-MS) is based on an in-silico derived peptide library covering the human virome in UniProtKB (331 viruses, 20,386 genomes, 121,977 peptides). A scoring algorithm (vProID score) is developed to assess the confidence of virus identification from proteomics data (https://github.com/RKI-ZBS/vPro-MS). In combination with diaPASEF-based data acquisition, this workflow enables the analysis of up to 60 samples per day. The specificity is determined to be >99,9% in an analysis of 221 plasma, swab and cell culture samples covering 17 different viruses. The sensitivity of this approach for the detection of SARS-CoV-2 in nasopharyngeal swabs corresponds to a PCR cycle threshold of 27 with comparable quantitative accuracy to metagenomics. vPro-MS enables the integration of untargeted virus identification in large-scale proteomic studies of biofluids such as human plasma to detect previously undiscovered virus infections in patient specimens.}, } @article {pmid40743118, year = {2025}, author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS}, title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0326358}, pmid = {40743118}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; }, abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.}, } @article {pmid40742122, year = {2025}, author = {Wu, H and Jiang, X and Xi, Y and Ning, S and Wu, H and Xin, W and Peng, W and Wang, S and Zhang, W}, title = {Genetic characterization of the marmot gut virome in high-altitude Qinghai Province and identification of novel viruses with zoonotic potential.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0029725}, doi = {10.1128/msphere.00297-25}, pmid = {40742122}, issn = {2379-5042}, abstract = {The high-altitude ecosystems of Qinghai Province, China, harbor unique viral communities shaped by extreme environmental conditions and host adaptations. This study presents a comprehensive genetic characterization of the marmot gut virome, revealing novel viral strains with zoonotic potential. Using viral metagenomics, we analyzed intestinal contents from 70 marmots collected from Chengduo and Maqin counties. Sequencing on the Illumina NovaSeq 6000 platform identified 19 viral genomes belonging to four major families: Adenoviridae, Astroviridae, Parvoviridae, and Picornaviridae, along with four novel circular Rep-encoding single-stranded DNA (CRESS DNA) viruses. Phylogenetic analyses demonstrated close relationships between marmot-derived strains and viruses from humans, bats, and other mammals, highlighting potential cross-species transmission risks. Notably, bat-associated adenoviruses showed closer phylogenetic proximity to human strains, while novel parvoviruses formed a distinct clade within the Dependoparvovirus genus. The discovery of a novel astrovirus with low sequence similarity to known genera underscores the need for taxonomic reclassification. Additionally, a novel picornavirus related to Sapelovirus and four divergent CRESS DNA viruses were identified, expanding our understanding of viral diversity in high-altitude rodents. These findings emphasize the role of marmots as viral reservoirs and highlight the importance of high-altitude ecosystems as hotspots for zoonotic pathogen emergence. This study provides critical insights into viral evolution, host adaptation, and zoonotic risks, advocating for integrated surveillance strategies to mitigate future spillover events.IMPORTANCEViruses are the most abundant and diverse biological entities on Earth, yet their presence in wildlife from extreme environments remains poorly understood. High-altitude ecosystems, shaped by harsh conditions like intense UV radiation and low oxygen levels, create unique settings for virus evolution. This study is the first to comprehensively profile the gut virome of marmots in Qinghai Province, uncovering novel viral strains and highlighting how extreme environments drive viral diversity. Marmots, as key species in these regions, can act as bridges for virus transmission among wildlife, livestock, and humans, posing zoonotic risks. Understanding these viral communities is essential for predicting and preventing future outbreaks. Our findings emphasize the urgent need for integrated, One Health-based surveillance strategies to safeguard both public health and biodiversity in fragile high-altitude ecosystems.}, } @article {pmid40739184, year = {2025}, author = {Tang, HB and Si, YX and Li, HD and Dang, W and Lu, HL}, title = {Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {466}, pmid = {40739184}, issn = {1471-2180}, support = {32471577//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Turtles/microbiology ; *Nitrites/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Stress, Physiological ; Intestines/microbiology ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; }, abstract = {BACKGROUND: Nitrite is one of the primary pollutants in high-density aquaculture systems, and may cause various toxic effects (e.g., oxidative damage, metabolic and immune dysregulation, histological inflammation, etc.) on economically important aquaculture species, such as echinoderms, crustaceans and fish. Nitrite can also disrupt the intestinal function and microbiota in some fish and amphibians. However, intestinal physiological and microbial responses of cultured turtles under nitrite stress were rarely explored.

METHOD: Twenty Mauremys reevesii juveniles were exposed to different nitrite levels and fed with a commercial diet. Their intestinal content samples were analyzed for microbial diversity and composition.

RESULTS: Nitrite exposure reduced intestinal microbial diversity, with lower α-diversity values in higher-concentration exposed turtles. It also changed the microbial composition. After exposure, the abundances of Bacteroidetes and Firmicutes decreased, but that of Proteobacteria increased at the phylum level. Similarly, abundances of some potentially beneficial bacterial genera, e.g., Prevotella_1, Christensenellaceae_R-7, Muribaculaceae_ge, were shown to decrease, but those of putatively pathogenic genera, e.g., Halomonas, Nesterenkonia, increased at the genus level. Furtherly, potentially altered metabolic pathways (e.g., biosynthesis of ansamycins and vancomycin group antibiotics) were revealed by functional predictions of intestinal microbiota.

CONCLUSION: This study highlighted intestinal microbial dysbiosis and prevalence of putatively pathogenic bacteria in cultured turtles under nitrite stress. Excessive levels of nitrite would alter the health status of aquatic animals by disrupting their intestinal microbiome.}, } @article {pmid40739125, year = {2025}, author = {Jiang, W and Xiong, M and Feng, S and Liu, Q and Chen, Y and Zou, S and Kang, D}, title = {Water content alters soil organic carbon metabolism via microbial traits in Tibetan alpine peatlands.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27793}, pmid = {40739125}, issn = {2045-2322}, support = {No. 2023NSFSC0143//the Natural Science Foundation of Sichuan Provence/ ; No. 31800458//the National Natural Science Foundation of China/ ; No. 2019-ZL-19//Sichuan Province Transportation Science and Technology Project: Research and Demonstration on Crucial Technologies of Wetland Eco-environment Protection Under the Influence of Highway Engineering on the Western Sichuan Plateau/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Tibet ; *Water/analysis ; Carbon Cycle ; Archaea/metabolism/genetics ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; Microbiota ; }, abstract = {Alpine peatlands on the eastern Tibetan Plateau are vital carbon sinks, with soil moisture playing a key role in peatland carbon cycling. However, they face disruptions in their carbon balance due to drought, which reduces soil water content. Therefore, this study investigated microbially driven water-carbon interactions through field surveys, laboratory incubations, and metagenomics. Soil drying contributes to changes in both the metabolic quotient (qCO2) and the microbial quotient (Cmic: Corg), as well as the microbial abundance. As the soil water content decreased, both qCO2 and Cmic: Corg exhibited an overall increasing trend. Moreover, soil water content had a more significant effect on soil bacteria, while its effect on fungi and archaea was minimal. Soil microbial carbon decomposition genes were also influenced by changes in soil water content. Next, we used RDA to analyze the relationship between soil respiration quotient values and microbial traits. The results revealed that Actinobacteria were strongly negatively correlated with qCO2, whereas Archaea and Candidatus_R were positively correlated with qCO2. Additionally, Cmic: Corg was closely linked to fungi, and both Proteobacteria and Acidobacteria exhibited positive correlations. qCO2 had a strong negative correlation with genes involved in the degradation of monosaccharides and hemicellulose, whereas Cmic: Corg was positively correlated with genes related to the degradation of cellulose and lignin. Moreover, droughts affected microbial residue carbon and associated carbon metabolic pathways. Therefore, changes in soil water content may be an important factor influencing carbon metabolism processes in peatlands. This study deepens our understanding of the effects of drought on soil metabolism and microbial dynamics in alpine peatlands and provides new insights into the microecological mechanisms of soil carbon cycling in these ecosystems in the context of global change.}, } @article {pmid40736894, year = {2025}, author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK}, title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2955}, number = {}, pages = {71-88}, doi = {10.1007/978-1-0716-4702-8_5}, pmid = {40736894}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; }, abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.}, } @article {pmid40736175, year = {2025}, author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q}, title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.}, journal = {Investigative ophthalmology & visual science}, volume = {66}, number = {9}, pages = {71}, pmid = {40736175}, issn = {1552-5783}, mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation & purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; }, abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.

METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.

RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).

CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.}, } @article {pmid40732945, year = {2025}, author = {Kulecka, M and Jaworski, P and Zeber-Lubecka, N and Bałabas, A and Piątkowska, M and Czarnowski, P and Frączek, B and Tarnowski, W and Mikula, M and Ostrowski, J}, title = {The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.}, journal = {Nutrients}, volume = {17}, number = {14}, pages = {}, pmid = {40732945}, issn = {2072-6643}, support = {2018/29/B/NZ7/00809//National Science Center/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Female ; *Metagenomics/methods ; Adult ; Feces/microbiology ; *Dysbiosis/microbiology/diagnosis ; Body Mass Index ; Middle Aged ; Bacteria/classification/genetics ; Workflow ; Case-Control Studies ; Young Adult ; }, abstract = {Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m[2]), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m[2]), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m[2]) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m[2] had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m[2]. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m[2] obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.}, } @article {pmid40731978, year = {2025}, author = {Garcia, M and Bruna, P and Duran, P and Abanto, M}, title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40731978}, issn = {2076-2607}, abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.}, } @article {pmid40731321, year = {2025}, author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M}, title = {The BeeBiome data portal provides easy access to bee microbiome information.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {198}, pmid = {40731321}, issn = {1471-2105}, mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; }, abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.}, } @article {pmid40731267, year = {2025}, author = {Xu, X and Qin, D and Qin, X and Gao, X and Li, C and Liu, X and Wu, G}, title = {Sustainable management of soil-borne disease: integrating fumigation with Andrographis paniculata residues to rebuild rhizosphere function.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {460}, pmid = {40731267}, issn = {1471-2180}, support = {32060639//the National Natural Science Foundation of China/ ; 202105AC160037, 202205AC160077//the Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Fumigation/methods ; *Andrographis/chemistry ; *Plant Diseases/microbiology/prevention & control ; *Plant Extracts/pharmacology/chemistry ; Metabolomics ; Fusarium/drug effects ; Soil/chemistry ; Microbiota/drug effects ; Metagenomics ; }, abstract = {Continuous pepper cropping induces soil-borne diseases and disrupts rhizosphere microecological balance. This study employed untargeted metabolomics and metagenomics to investigate treatment effects on rhizosphere metabolic reprogramming and microbe-metabolite interactions. Aqueous and ethanolic extracts of Andrographis paniculata residues (TCMR) were rich in flavonoids, terpenoids, and phenolic acids, exhibiting significant inhibition against soil-borne pathogens (Fusarium oxysporum, Fusarium solani, and others; >70% inhibition at high doses). While single fumigation (W1, M1) transiently suppressed pathogens, it disrupted rhizosphere metabolic homeostasis. In contrast, combined fumigation-TCMR treatments (WC, MC) enhanced plant stress resistance, stabilized membrane integrity, and reshaped microbial communities by modulating amino acid, lipid, and phenylpropanoid biosynthesis pathways. Microbe-metabolite network analysis revealed that coupling carbon-nitrogen cycling with redox homeostasis drives soil microecological optimization. This integrated strategy provides a sustainable solution for continuous cropping obstacles through synergistic metabolic reprogramming and microbiome reconstruction.}, } @article {pmid40730965, year = {2025}, author = {Clark-Boucher, D and Coull, BA and Reeder, HT and Wang, F and Sun, Q and Starr, JR and Lee, KH}, title = {Group-wise normalization in differential abundance analysis of microbiome samples.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {196}, pmid = {40730965}, issn = {1471-2105}, support = {U01 HD052104/HD/NICHD NIH HHS/United States ; T32 GM135117/GM/NIGMS NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; T32GM135117/GM/NIGMS NIH HHS/United States ; R03 DE027486/DE/NIDCR NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R01 GM126257/GM/NIGMS NIH HHS/United States ; U01 HD052102/HD/NICHD NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; P01 HD103133/HD/NICHD NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome ; Algorithms ; *Metagenomics/methods ; Humans ; }, abstract = {BACKGROUND: A key challenge in differential abundance analysis (DAA) of microbial sequencing data is that the counts for each sample are compositional, resulting in potentially biased comparisons of the absolute abundance across study groups. Normalization-based DAA methods rely on external normalization factors that account for compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled to maintain the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in DAA by re-conceptualizing normalization as a group-level task. We present two new normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS).

RESULTS: G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings. The two novel methods also maintain the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the DAA method MetagenomeSeq.

CONCLUSION: Compared with other methods for normalizing compositional sequence count data prior to DAA, the proposed group-level normalization frameworks offer more robust statistical inference. With a solid mathematical foundation, validated performance in numerical studies, and publicly available software, these new methods can help improve rigor and reproducibility in microbiome research.}, } @article {pmid40730483, year = {2025}, author = {Zhong, H and Song, Y and Hu, S and Zhang, C and Li, L}, title = {Metagenomics-Metabolomics Reveals the Alleviation of Indole-3-Ethanol on Radiation-Induced Enteritis in Mice.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2502037}, pmid = {40730483}, issn = {1738-8872}, mesh = {Animals ; *Indoles/pharmacology/metabolism ; *Enteritis/drug therapy/etiology/metabolism/microbiology/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Anti-Inflammatory Agents/pharmacology ; Colon/pathology/drug effects/radiation effects ; Cytokines/metabolism ; Interleukin-17/metabolism ; }, abstract = {Indole-3-ethanol (IEt), a small molecule metabolite from intestinal microbial tryptophan metabolism, has been established to have anti-inflammatory properties. However, its effect on radiation-induced enteritis has not been reported. Here, we aim to explore the effects and potential mechanisms of IEt on radiation enteritis. C57BL/6J mice were orally administered an IEt solution before radiation exposure. Inflammatory factors, including IL-17A, IFN-γ, IL-6 and IL-1β, were detected using enzyme-linked immunosorbent assay. Colonic histopathology was assessed through H&E staining. Subsequently, gut microbiota and its metabolites were analyzed using metagenomics and metabolomics. The results suggested that IEt alleviated radiation-induced enteritis, as evidenced by improved colonic structural integrity, decreased levels of pro-inflammatory factors like IL-17A, and the restoration of intestinal microecological and metabolic balance. IEt enriched the abundance of Lachnospiraceae family members, particularly the genus Roseburia - a known anti-inflammatory commensal. In addition, IEt upregulated the levels of metabolites with anti-inflammatory effects such as indole-3-carbinol, pteridine, and pyropheophorbide-a. Furthermore, Roseburia was significantly positively correlated with indole-3-carbinol and negatively correlated with the pro-inflammatory factor IL-17A. Therefore, IEt may alleviate radiation enteritis through Roseburia-indole-3-carbinol and Roseburia-IL-17A axes. This study revealed the potential mechanisms by which IEt alleviated radiation enteritis, providing a potential protective candidate for radiation enteritis.}, } @article {pmid40728669, year = {2025}, author = {Priyadarsini, M and Dhoble, AS}, title = {Combination of flow cytometry and metagenomics to monitor the effect of raw vs digested manure on microbial diversity in anaerobic digestion of Napier grass.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {8}, pages = {963}, pmid = {40728669}, issn = {1573-2959}, support = {SPARC/2019-2020/P1570/SL//Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; }, mesh = {*Manure/microbiology ; Flow Cytometry ; Metagenomics ; *Poaceae/microbiology ; Anaerobiosis ; *Microbiota ; Biofuels ; Bacteria ; Archaea ; Animals ; }, abstract = {Microbiomes play a crucial role in anaerobic digestion (AD), by degrading the complex lignocellulosic biomass leading to biomethane production. This study emphasizes the role of microbial diversity and its impact on the digester's performance with raw (CD) and digested manure (ADS) as a source of microbiome and Napier grass (NG) as feedstock. The integration of flow cytometry and metagenomics provides a novel perspective on microbial dynamics during anaerobic digestion. Initially, the inocula (ADS and CD) had 354 bacterial and 8 archaeal genera in common that decreased to 39 bacteria and 1 archaeon at the end of experiment, indicating significant shift in microbial diversity during the process. Metagenome sequencing showed that Clostridium was the most abundant genera in NG digested with ADS, while Prevotella was in NG digested with CD. An approximately 2.45% increase in Clostridium in NG digested with ADS led to VFA accumulation and pH drop, inhibiting methanogens and lower biogas production. Most of the flow cytometric populations showed positive correlation with Prevotella suggesting its key role in breaking down of complex substrate. The population 2, 3, and 5 positively correlated to biogas production. NG digested with CD produced nearly twice biogas yield (1064.33 ± 119.97 mL) compared to ADS (508 ± 20.95 mL) which corresponds to the enhanced microbial activity in CD. These findings suggest that microbiome of CD might be better acclimatized for NG degradation than ADS as NG is often used as cattle fodder.}, } @article {pmid40728577, year = {2025}, author = {Raziq, MF and Manzoor, H and Kayani, MUR}, title = {Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.}, journal = {Current microbiology}, volume = {82}, number = {9}, pages = {419}, pmid = {40728577}, issn = {1432-0991}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology ; *Immunotherapy/methods ; *Lung Neoplasms/therapy/microbiology/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; }, abstract = {Lung cancer remains the second most commonly diagnosed cancer and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC), accounting for approximately 85% of lung cancer cases, is the most prevalent form. Treatment options for NSCLC include surgery, radiation therapy, chemotherapy, immunotherapy, and targeted drug therapies. Among these, immune checkpoint inhibitors targeting PD-1/PD-L1 have demonstrated significant potential, particularly in improving treatment outcomes. However, their clinical efficacy is impeded by challenges such as toxicity, resistance development, and variable patient responses. Emerging evidence highlights the critical role of the gut microbiome as an important modulator of immune responses in NSCLC, particularly in the context of anti-PD-1/PD-L1 therapies. Specific gut microbes, such as Akkermansia muciniphila, have been associated with improved responses to immunotherapy, suggesting that modulation of the gut microbiome may enhance treatment outcomes. This review discusses the current understanding of the influence of gut microbiome on NSCLC and its potential to improve the clinical efficacy of anti-PD-1/PD-L1 therapies. By integrating microbiome-based insights into personalized treatment strategies, we can overcome the limitations of current immunotherapy approaches and optimize patient outcomes. This review aims to serve as a resource for the scientific community by providing insights into how modulation of gut microbiome may enhance treatment outcomes in NSCLC patients receiving anti-PD-1/PD-L1 immunotherapy.}, } @article {pmid40726156, year = {2025}, author = {Yang, S and Huang, X and Li, X and Feng, J and Chen, P and Cao, Z and He, L and Li, C and Li, Z and Xie, M}, title = {Aloe vera polysaccharides mitigate high-fat high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice via regulation of lipid metabolism and gut microbiota.}, journal = {Food & function}, volume = {16}, number = {16}, pages = {6671-6686}, doi = {10.1039/d5fo01995h}, pmid = {40726156}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Atherosclerosis/drug therapy/metabolism/etiology ; Diet, High-Fat/adverse effects ; Mice ; *Lipid Metabolism/drug effects ; *Aloe/chemistry ; Male ; *Polysaccharides/pharmacology/administration & dosage ; Apolipoproteins E/genetics ; Mice, Inbred C57BL ; RAW 264.7 Cells ; Disease Models, Animal ; }, abstract = {Cardiovascular diseases are leading causes of death globally, often manifesting after years of atherosclerosis (AS) progression. In this study, we investigated the atheroprotective effects of three different sources of glucomannan, Dendrobium officinale polysaccharide, Konjac glucomannan, and Aloe vera polysaccharide (AVP), using an in vitro ox-LDL-induced foam cell model and an in vivo high-fat high-cholesterol diet-fed ApoE[-/-] mouse model. Both settings indicate that AVP exerts the most significant atheroprotective effects. It inhibits lipid absorption and enhances the regulation of lipid homeostasis by the liver X receptor, thereby suppressing the formation of foam cells. It can also alleviate ox-LDL-induced oxidative stress and apoptosis in RAW 264.7 cells. Animal experiments show that AVP can prevent the formation of atherosclerotic plaques and coronary artery fibrosis, while also reducing circulating IL-1β levels. Furthermore, liver transcriptomic analysis shows that AVP inhibits inflammation and promotes bile acid excretion and transport by upregulating the farnesoid X receptor. Additionally, metagenomic analysis indicates that AVP can significantly reverse the microbial alterations associated with AS. Specific gut microbes, such as Prevotella, may partially mediate the effects of AVP through the gut-liver axis. This is the first study to report the atheroprotective effects of AVP, demonstrating that it alleviates atherosclerosis by restoring lipid metabolism homeostasis and modulating the gut microbiome.}, } @article {pmid40724992, year = {2025}, author = {Rušanac, A and Škibola, Z and Matijašić, M and Čipčić Paljetak, H and Perić, M}, title = {Microbiome-Based Products: Therapeutic Potential for Inflammatory Skin Diseases.}, journal = {International journal of molecular sciences}, volume = {26}, number = {14}, pages = {}, pmid = {40724992}, issn = {1422-0067}, support = {NPOO.C3.2.R3-I1.04.0240//European Regional Development Fund/ ; KK.01.2.1.02.0137//European Regional Development Fund/ ; IP.1.1.03.0157//European Regional Development Fund/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; *Skin Diseases/microbiology/therapy ; Dysbiosis/microbiology/therapy ; Skin/microbiology ; Animals ; Psoriasis/microbiology/therapy ; Dermatitis, Atopic/microbiology/therapy ; }, abstract = {Maintaining a balanced skin microbiota is essential for skin health, whereas disruptions in skin microbiota composition, known as dysbiosis, can contribute to the onset and progression of various skin disorders. Microbiota dysbiosis has been associated with several inflammatory skin conditions, including atopic dermatitis, seborrheic dermatitis, acne, psoriasis, and rosacea. Recent advances in high-throughput sequencing and metagenomic analyses have provided a deeper understanding of the skin microbial communities in both health and disease. These discoveries are now being translated into novel therapeutic approaches aimed at restoring microbial balance and promoting skin health through microbiome-based interventions. Unlike conventional therapies that often disrupt the microbiota and lead to side effects or resistance, microbiome-based products offer a more targeted strategy for preventing and managing inflammatory skin diseases. These products, which include probiotics, prebiotics, postbiotics, and live biotherapeutic agents, are designed to modulate the skin ecosystem by enhancing beneficial microbial populations, suppressing pathogenic strains, and enhancing immune tolerance. As a result, they represent a promising class of products with the potential to prevent, manage, and even reverse inflammatory skin conditions. However, realizing the full therapeutic potential of microbiome-based strategies in dermatology will require continued research, robust clinical validation, and clear regulatory frameworks.}, } @article {pmid40723458, year = {2025}, author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Probanza, A and Jiménez-Gómez, PA}, title = {Use of Bacillus pretiosus and Pseudomonas agronomica for the Synthesis of a Valorized Water Waste Treatment Plant Waste as a Biofertilizer Intended for Quercus pyrenaica L. Fertigation.}, journal = {Biology}, volume = {14}, number = {7}, pages = {}, pmid = {40723458}, issn = {2079-7737}, support = {TED2021-132285A-I00//Next Generation Funds/ ; }, abstract = {The loss of hectares of forest areas has become a global issue that has worsened over recent years due to unsustainable human activities. In a context of limited availability of productive land, it is urgent to adopt efficient strategies to recover the affected natural areas. Actions based on a circular economy, such as the use of organic chemical matrices recovered from water waste treatment plant waste, have proven to be effective. In this regard, the addition of plant growth-promoting bacteria (PGPB), such as Bacillus pretiosus and Pseudomonas agronomica, can contribute to the chemical treatment, favoring the recovery of soils, accelerating the recovery of vegetation cover, and inducing an increase in biodiversity. In this research, the effect of bio-fertigation under controlled laboratory conditions in Quercus pyrenaica is evaluated. After a thirty-six-week trial, the biometric and nutritional parameters of the plants were harvested and measured, and the diversity and composition of the metagenomes of their rhizospheres were evaluated. As well, the cenoantibiogram and the metabolic diversity were measured. The results showed that the use of these biofertilizers increased the variables related to plant production, quality of plant composition as an indirect means of their resilience, as well as an increase in rhizospheric microbial diversity and a reduction in their MIC resistance to the most widely used antibiotics. For all these reasons, the use of the biofertilizer result of the combination of WWTP waste, Bacillus pretiosus, and Pseudomonas agronomica is postulated as an environmentally friendly strategy that can contribute to the recovery of potential oak forest areas.}, } @article {pmid40721426, year = {2025}, author = {Yang, Y and Ye, M and Song, Y and Xing, W and Zhao, X and Li, Y and Shen, J and Zhou, J and Arikawa, K and Wu, S and Song, Y and Xu, N}, title = {Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {146}, pmid = {40721426}, issn = {2055-5008}, support = {2020YFC2003700//National Key R&D Plan/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 20Z11901000, 20DZ2261200, 20XD1401200, 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; SHDC2020CR5010-002//Clinical Research Plan of SHDC/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; ZY(2021-2023)-0207-01//Shanghai Municipal Health Commission and Shanghai Municipal Administrator of Traditional Chinese Medicine/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy ; *Immunotherapy/methods ; Animals ; *Lung Neoplasms/therapy/microbiology/drug therapy ; Mice ; *Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Male ; Metagenomics ; Middle Aged ; Aged ; Dysbiosis/microbiology ; Antineoplastic Agents/therapeutic use ; }, abstract = {The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung cancer (NSCLC) patients treated with chemo-immunotherapy, comparing responders and non-responders using 16S rRNA sequencing. Responders showed higher microbial richness and abundance of specific genera like Faecalibacterium and Subdoligranulum, and the phylum Firmicutes. Support vector machine (SVM), a machine learning model based on microbial composition, predicted treatment efficacy with the area under the curve (AUC) values of 0.763 for genera and 0.855 for species. Metagenomic analysis revealed significant differences in metabolic pathways, with responders exhibiting higher short-chain fatty acids (SCFAs) production. Fecal microbiota transplantation (FMT) and SCFAs supplementation in mouse models enhanced treatment efficacy by promoting effector T cell activity in tumors. Our study suggests that gut microbiota, through SCFAs production, regulates chemo-immunotherapy efficacy, offering new strategies to improve NSCLC treatment outcomes.}, } @article {pmid40716139, year = {2025}, author = {Lemos-Lucumi, CA and Cárdenas-Hernández, V and Toro-Perea, N}, title = {Metagenomic and metatranscriptomic exploration of Avicennia germinans L.: Endophytic microbiome of leaves and roots.}, journal = {Microbiological research}, volume = {300}, number = {}, pages = {128287}, doi = {10.1016/j.micres.2025.128287}, pmid = {40716139}, issn = {1618-0623}, mesh = {*Endophytes/genetics/classification/isolation & purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Avicennia/microbiology ; *Microbiota ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Gene Expression Profiling ; Transcriptome ; Metagenome ; }, abstract = {Mangroves are productive coastal ecosystems with extreme environmental conditions of temperature, salinity and anthropogenic pollution. Their associated microbiota plays an essential role in plant survival, yet their functional dynamics remain poorly understood. This study characterizes the endophytic microbiome of Avicennia germinans L. in the Buenaventura Bay mangrove ecosystem (Colombia), using a combined metagenomic and metatranscriptomic approach. Distinct microbial communities were observed in leaves and pneumatophores. Root-associated endophytes exhibited higher taxonomic richness and greater transcriptional activity. Functional gene expression revealed enrichment of pathways related to osmotic and oxidative stress responses, hydrocarbon degradation, nitrogen metabolism, and ion homeostasis. The expression of efflux pumps, NADH dehydrogenase, cytochromes, chaperones, H[+]-ATPases, and H[+]/Na[+] antiporters suggest active microbial participation in salinity, heavy metal, xenobiotics and stress resistance. These findings highlight the adaptive versatility of the endophytic microbiome in A. germinans and support its potential for biotechnological applications in stress resistance and bioremediation.}, } @article {pmid40720840, year = {2025}, author = {Slizovskiy, IB and Gaire, TN and Ferm, PM and Odland, CA and Dee, SA and Nerem, J and Bravo, JE and Kimball, AD and Boucher, C and Noyes, NR}, title = {Reducing skin microbiome exposure impacts through swine farm biosecurity.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf062}, pmid = {40720840}, issn = {2047-217X}, support = {/NH/NIH HHS/United States ; 1R01AI141810-01//National Institute of Allergy and Infectious Diseases/ ; 5U54OH010170-13A/OH/NIOSH CDC HHS/United States ; }, mesh = {*Microbiota ; *Skin/microbiology ; Animals ; Swine/microbiology ; Humans ; Farms ; *Biosecurity ; *Occupational Exposure ; Female ; Male ; Adult ; Bacteria/genetics/classification/isolation & purification ; Longitudinal Studies ; Animal Husbandry ; Skin Microbiome ; }, abstract = {BACKGROUND: Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohort within the US livestock labor force, as they have direct daily contact with pigs and undertake mandatory biosecurity interventions. However, investigating this occupational cohort is challenging, particularly within tightly regulated commercial swine operations. Thus, little is known about the impacts of animal exposure and biosecurity protocols on the swine worker microbiome. We obtained unique samples from US swine workers, using a longitudinal study design to investigate temporal microbiome dynamics.

RESULTS: We observed a significant increase in bacterial DNA load on worker skin during the workday, with concurrent changes in the composition and abundance of microbial taxa, resistance genes, and mobile genetic elements. However, mandatory showering at the end of the workday partially returned the skin's microbiome and resistome to their original state.

CONCLUSIONS: These novel results from a human cohort demonstrate that existing biosecurity practices can ameliorate work-associated microbiome impacts.}, } @article {pmid40719990, year = {2025}, author = {Naqvi, SAH and Umar, UUD and Rehman, AU}, title = {Beneficial communities from core bacterial microbiota of Oryza sativa L. soil and leaves perform dynamic role in growth promotion and suppression of bacterial leaf blight.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {8}, pages = {285}, pmid = {40719990}, issn = {1573-0972}, mesh = {*Oryza/microbiology/growth & development ; *Soil Microbiology ; *Plant Leaves/microbiology/growth & development ; Xanthomonas/pathogenicity/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Plant Diseases/microbiology/prevention & control ; *Microbiota/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Pakistan ; Biological Control Agents ; Soil/chemistry ; Metagenomics ; Phylogeny ; }, abstract = {Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), severely threatens global rice production, highlighting the urgent need for sustainable alternatives to chemical pesticides. This study investigates the rhizosphere and phyllosphere microbiomes of Oryza sativa in Punjab, Pakistan, to identify native biocontrol agents (BCAs) with potential to suppress BLB. Using 16S rRNA amplicon sequencing (V3-V9 regions), we analyzed soil and leaf samples from 10 agricultural districts. Microbial diversity, community structure, and functional potential were assessed via bioinformatics tools (QIIME 2, DADA2, PICRUSt2), with a focus on taxa antagonistic to Xoo. Healthy rhizospheres exhibited significantly higher alpha diversity (Shannon index: 6.8 vs. 4.2 in leaves; *p* < 0.001), dominated by copiotrophic taxa (Proteobacteria, Bacteroidetes) linked to organic inputs and root exudates. Diseased soils favored oligotrophic Actinobacteria and Chloroflexi. Functional metagenomics revealed enrichment of siderophore biosynthesis, antibiotic production, and nutrient-cycling genes in healthy soils. Antagonistic genera (Bacillus, Pseudomonas, Streptomyces) demonstrated chitinase and surfactin activity against Xoo, while diseased samples showed elevated Xanthomonas and Erwinia abundances correlating with BLB severity. Native BCAs outperformed non-native strains in colonization and nutrient competition, highlighting their adaptability to local agroecological conditions. Our findings position native BCAs as pivotal tools for BLB suppression and sustainable agriculture, reducing reliance on synthetic chemicals. Field trials confirmed that microbial consortia formulations reduced BLB incidence by 40% and increased yield by 18%. These findings highlight the potential of microbiome-driven strategies to mitigate BLB, reduce chemical reliance, and foster sustainable agricultural practices. Future work should integrate multi-omics approaches to optimize microbial solutions for climate resilience and scale their adoption through policy frameworks.}, } @article {pmid40719366, year = {2025}, author = {Wang, X and Wang, N and Gao, T and Zhang, Y and Fu, Z and Zhao, Y and Huang, Y and Zheng, X and Gao, X and Lu, L and Yang, L}, title = {Symptom-specific gut microbial and metabolic profiles in ADHD reveal SCFA deficiency as a Key pathogenic mechanism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2537755}, pmid = {40719366}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Animals ; Humans ; Mice ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Fecal Microbiota Transplantation ; Child ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metabolome ; Adolescent ; Metabolomics ; }, abstract = {Previous evidence links gut microbiota to attention-deficit/hyperactivity disorder (ADHD) through the gut-brain axis. However, the specific microbiota contributing to symptoms remain unclear. To characterize the gut microbial profile related to different symptoms and explore the mediation mechanism between microbiota alterations and the core ADHD symptoms, we conducted shotgun metagenomic sequencing and fecal metabolomics analysis on 94 ADHD patients and 94 age- and gender-matched controls. Microbial characteristics of three subgroups exhibiting different ADHD core symptom presentations were analyzed. We developed a metabolic model and conducted causal mediation analyses to examine how metabolites connect the microbiota to the symptoms. Fecal microbiota transplantation in mice was employed to validate the findings. The redundancy analysis identified ADHD symptoms as environmental gradients and explained the changes in beta diversity (F = 1.345, pFDR = 0.015). Greater gut microbial alterations were observed in combined presentations (ADHD-C). Several beneficial bacteria involved in short-chain fatty acid synthesis were found to be downregulated, with Lactobacillus sanfranciscensis notably linked to all three core symptoms (p.adj = 1.04E-13; p.adj = 5.07E-07; p.adj = 2.61E-05). Various taxa, functional pathways, and metabolites associated with specific ADHD symptom domains were identified. Imidazoleacetic acid partially mediated the effects between Lactobacillus sanfranciscensis and inattention (p = 0.012). In mice subjected to feces from ADHD patients with a low abundance of Lactobacillus sanfranciscensis, treatment with this strain greatly improved both hyperactivity (t = 2.665, p = 0.0237) and inattention (t = 2.389, p = 0.0380), while acetate supplementation only alleviated inattention (t = 2.362, p = 0.0398). Our findings suggest that different ADHD symptoms were related to common and different gut microbiota and metabolites. Fecal microbiota transplantation in mice validated the hypothesis that gut microbial composition affects ADHD symptoms through metabolic alterations. This study provides more insight into the mechanisms underlying metabolic disturbances in ADHD and elucidates the role of gut microbiota in these processes.}, } @article {pmid40715283, year = {2025}, author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM}, title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {27297}, pmid = {40715283}, issn = {2045-2322}, mesh = {*Biofilms/growth & development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; }, abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.}, } @article {pmid40715043, year = {2025}, author = {Duchesneau, K and Aldeguer-Riquelme, B and Petro, C and Makke, G and Green, M and Tfaily, M and Wilson, R and Roth, SW and Johnston, ER and Kluber, LA and Schadt, CW and Trejo, JB and Callister, SJ and Purvine, SO and Chanton, JP and Hanson, PJ and Tringe, S and Eloe-Fadrosh, E and Glavina Del Rio, T and Konstantinidis, KT and Kostka, JE}, title = {Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6869}, pmid = {40715043}, issn = {2041-1723}, support = {DE-SC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Microbiota/genetics/physiology ; Methane/metabolism ; Metagenome ; Carbon/metabolism ; Climate Change ; Bacteria/metabolism/genetics/classification ; Global Warming ; Ecosystem ; Electrons ; }, abstract = {The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.}, } @article {pmid40714398, year = {2025}, author = {Wu, L and Yan, M and Huang, X and Liao, H and Bao, D and Ge, Y and Wang, S and Xia, X}, title = {Temperature-mediated shift from competitive to facilitative interactions between lactic acid bacteria and bacillus species in daqu fermentation: Insights from metagenomics, dual RNA-seq, and coculture analysis.}, journal = {International journal of food microbiology}, volume = {442}, number = {}, pages = {111352}, doi = {10.1016/j.ijfoodmicro.2025.111352}, pmid = {40714398}, issn = {1879-3460}, abstract = {Daqu, a pivotal starter that defines the flavor profile and quality of Baijiu, undergoes dynamic temperature changes during its production, significantly influencing the microbial community structure and function. Although the importance of fermentation temperature in shaping microbial biodiversity is well-recognized, its impact on microbial interaction dynamics and the underlying mechanisms remains poorly understood. This study integrates metagenomics, dual RNA-seq, and coculture experiments to elucidate temperature-dependent microbial interactions during Daqu fermentation. Metagenomic analysis revealed that lactic acid bacteria (LAB) and Bacillus are dominant genera with distinct thermal preferences that nevertheless coexist throughout the fermentation process. Elevated temperature stress was found to enhance positive microbial interactions within the Daqu ecosystem. Dual RNA-seq analysis uncovered temperature-responsive gene expression patterns associated with oxidative stress, metabolic capacity, and environmental information processing in representative LAB and Bacillus strains. Guided by these multi-omics findings, co-culture assays demonstrated a temperature-dependent shift in microbial interaction modes. At 30 °C, Lactococcus lactis secretes lactic acid that inhibits the growth of Bacillus subtilis, whereas at 50 °C, B. subtilis alleviates oxidative stress in L. lactis by producing cobalamin, thereby enabling short-term rescue and sustained coexistence over serial transfers. These findings provide critical insights into the temperature-driven modulation of microbial interactions, enhancing the precision and manageability of the Daqu fermentation process.}, } @article {pmid40713905, year = {2025}, author = {Zhou, J and Zhang, CJ and Zou, D and Gu, C and Li, M}, title = {Magnetite drives microbial community restructuring and stimulates aceticlastic methanogenesis of type II Methanosarcina in mangrove sediments.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {174}, pmid = {40713905}, issn = {2049-2618}, support = {42207144//National Natural Science Foundation of China/ ; 32225003, 32393971, and 32393970//National Natural Science Foundation of China/ ; 2024A1515010843//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; KCXFZ20240903092800002//Shenzhen Science and Technology Program/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; }, mesh = {*Methane/metabolism/biosynthesis ; *Ferrosoferric Oxide/pharmacology/metabolism ; *Geologic Sediments/microbiology ; Wetlands ; *Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects ; *Microbial Consortia/drug effects ; *Microbiota/drug effects ; Acetates/metabolism ; Lactic Acid/metabolism ; }, abstract = {BACKGROUND: Mangrove wetlands are critical hotspots of methane emissions, yet the role of naturally occurring minerals in shaping their microbial communities and methanogenic processes is poorly understood. Magnetite, a common iron mineral in soils and sediments, has been reported to enhance aceticlastic methanogenesis and facilitate syntrophic methanogenesis. In this study, we integrated multi-omic profiling with cultivation-based approaches to investigate the impact of magnetite on methanogenesis of microbial consortia derived from mangrove sediments, using lactate as a substrate.

RESULTS: Across five serial transfers, mangrove microbial consortia converted lactate to propionate and acetate, which were subsequently degraded into methane. Magnetite addition significantly stimulated methane production, leading to notable changes in community structure, particularly for aceticlastic methanogens, with Methanosarcina predominating in the magnetite-amended cultures and Methanothrix in controls. Four Methanosarcina strains T3, T4, T13, and MeOH were subsequently isolated from magnetite-amended cultures. Combined analyses of metagenome-assembled genomes and the genomes of these isolates revealed that the enriched Methanosarcina in magnetite-amended cultures belonged to type II deficient in hydrogenotrophic methanogenesis pathway. Metatranscriptomic analyses suggested that magnetite addition stimulated aceticlastic methanogenesis of type II Methanosarcina and hydrogenotrophic methanogenesis of Methanomicrobiales in the consortia. Furthermore, pure culture experiments confirmed that magnetite stimulated aceticlastic methanogenesis by Methanosarcina sp. T3, although its gene expression patterns differed from those observed in the microbial consortia. Additionally, Methanofastidiosales, an uncultured archaeal lineage possessing H2-dependent methylotrophic methanogenesis, was detected in all transfers.

CONCLUSIONS: Our findings demonstrate that magnetite alters methanogenic consortia in mangrove sediments, selectively stimulating aceticlastic methanogenesis of type II Methanosarcina and modulating hydrogenotrophic activity in Methanomicrobiales. By integrating multi-omics analyses with pure culture validation, we demonstrate, for the first time, that magnetite directly enhances the aceticlastic methanogenesis of type II non-hydrogenotrophic Methanosarcina. This study provides new insights into the influence of magnetite on complex microbial consortia, offers a deeper understanding of the physiology of type II non-hydrogenotrophic Methanosarcina, and advances knowledge of mineral-mediated regulation of methanogenic networks in anoxic environments. Video Abstract.}, } @article {pmid40713701, year = {2025}, author = {Bhardwaj, K and Niharika, and Garg, A and Jain, A and Kumar, M and Datt, M and Singh, V and Vrati, S}, title = {Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {254}, pmid = {40713701}, issn = {1743-422X}, support = {BT/PR18657/BIC/101/507/2016//Department of Biotechnology, Ministry of Science and Technology, India/ ; JCB/2021/000015//Science and Engineering Research Board/ ; }, mesh = {Humans ; *Genome, Viral ; *Metagenome ; Feces/virology ; *Virome ; Metagenomics ; *Gastrointestinal Tract/virology ; *Viruses/genetics/classification/isolation & purification ; Gastrointestinal Microbiome ; Phylogeny ; }, abstract = {Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains uncharacterized. In this study, we mined a collection of 1090 metagenome assembled "high quality" viral genomes (> 90% completeness, as determined by CheckV) derived from human fecal samples. Sequence analysis revealed eight new species spanning seven genera within the class, Caudoviricetes and nineteen new species from fourteen genera within the ssDNA virus family, Microviridae. Additionally, four "high quality" genomes were not found in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation and KEGG pathway analysis of the "high-quality" genomes identified seven core genes (antB, dnaB, DNMT1, DUT, xlyAB, xtmB and xtmA) associated with metabolism and fundamental viral processes. Moreover, genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also detected. Host prediction analysis suggest bacterial hosts for approximately 40% of the genomes. Overall, this study reports the discovery of novel viral genomes and provides a comprehensive genome profiling of human gut viruses in a subpopulation from India. These findings serve as a foundation for future biological investigations to elucidate the role of these viruses in host physiology.}, } @article {pmid40711892, year = {2025}, author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and , }, title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.}, journal = {The Journal of general virology}, volume = {106}, number = {7}, pages = {}, doi = {10.1099/jgv.0.002111}, pmid = {40711892}, issn = {1465-2099}, mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; }, abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.}, } @article {pmid40707990, year = {2025}, author = {Drevland, OM and de Muinck, EJ and Trosvik, P and Hammerstad, M and Kvitne, KE and Midtvedt, K and Åsberg, A and Robertsen, I}, title = {Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {169}, pmid = {40707990}, issn = {2049-2618}, support = {315792//Norges Forskningsråd/ ; 315792//Norges Forskningsråd/ ; }, mesh = {*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism ; *Kidney Transplantation ; Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Immunosuppressive Agents/pharmacokinetics/therapeutic use ; Middle Aged ; Feces/microbiology ; Adult ; Transplant Recipients ; Glucuronidase/metabolism/genetics ; Glucuronides/metabolism ; Metagenomics/methods ; *Enterohepatic Circulation ; }, abstract = {BACKGROUND: The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data.

RESULTS: We compared the fecal microbiomes of kidney transplant recipients (n = 21) both pre- and post-transplantation to healthy individuals (n = 15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific β-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles.

CONCLUSIONS: We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients. Video Abstract.}, } @article {pmid40707831, year = {2025}, author = {Sereika, M and Mussig, AJ and Jiang, C and Knudsen, KS and Jensen, TBN and Petriglieri, F and Yang, Y and Jørgensen, VR and Delogu, F and Sørensen, EA and Nielsen, PH and Singleton, CM and Hugenholtz, P and Albertsen, M}, title = {Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.}, journal = {Nature microbiology}, volume = {10}, number = {8}, pages = {2018-2030}, pmid = {40707831}, issn = {2058-5276}, support = {130690//Villum Fonden (Villum Foundation)/ ; 50093//Villum Fonden (Villum Foundation)/ ; }, mesh = {*Soil Microbiology ; Phylogeny ; Metagenomics/methods ; *Genome, Bacterial ; *Bacteria/genetics/classification/isolation & purification ; Geologic Sediments/microbiology ; *Biodiversity ; Ecosystem ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Nanopore Sequencing ; Sequence Analysis, DNA/methods ; }, abstract = {The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these environments. Here we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected during the Microflora Danica project, yielding genomes of 15,314 previously undescribed microbial species, recovered using our custom mmlong2 workflow. The recovered microbial genomes span 1,086 previously uncharacterized genera and expand the phylogenetic diversity of the prokaryotic tree of life by 8%. The long-read assemblies also enabled the recovery of thousands of complete ribosomal RNA operons, biosynthetic gene clusters and CRISPR-Cas systems. Furthermore, the incorporation of the recovered genomes into public genomic databases substantially improved species-level classification rates for soil and sediment metagenomic datasets. These findings demonstrate that long-read sequencing allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain an untapped source of biodiversity.}, } @article {pmid40707722, year = {2025}, author = {Mangnier, L and Bodein, A and Mariaz, M and Mathieu, A and Scott-Boyer, MP and Vashist, N and Bramble, MS and Droit, A}, title = {A systematic benchmark of integrative strategies for microbiome-metabolome data.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1100}, pmid = {40707722}, issn = {2399-3642}, support = {K01 TW011772/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; *Gastrointestinal Microbiome ; Benchmarking ; *Metagenomics/methods ; *Microbiota ; Computational Biology/methods ; }, abstract = {The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.}, } @article {pmid40707492, year = {2025}, author = {Villette, R and Novikova, PV and Laczny, CC and Mollenhauer, B and May, P and Wilmes, P}, title = {Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {142}, pmid = {40707492}, issn = {2055-5008}, support = {863664//HORIZON EUROPE European Research Council/ ; 863664//HORIZON EUROPE European Research Council/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; }, mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gene Regulatory Networks ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Aged ; Middle Aged ; }, abstract = {Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.}, } @article {pmid40707215, year = {2025}, author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE}, title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.}, journal = {Microbes and environments}, volume = {40}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME24067}, pmid = {40707215}, issn = {1347-4405}, mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Archaea/classification/metabolism/genetics/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; }, abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.}, } @article {pmid40703671, year = {2025}, author = {Wang, Y and Lu, J and Dai, W and Yang, S}, title = {Jian-Pi-Yi-Shen formula improves kidney function by regulating gut microbiome in rats with chronic kidney disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1526863}, pmid = {40703671}, issn = {2235-2988}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; Rats ; *Kidney/drug effects/physiopathology ; Disease Models, Animal ; Feces/microbiology ; Male ; Creatinine/blood ; Rats, Sprague-Dawley ; Metagenomics ; Medicine, Chinese Traditional ; }, abstract = {INTRODUCTION: Recent studies have underscored the role of interactions between Traditional Chinese Medicine (TCM) and the gut microbiome (GM) in mediating therapeutic effects. Jian-Pi-Yi-Shen Formula (JPYSF) has shown efficacy in ameliorating chronic kidney disease (CKD) symptoms, but its mechanisms via GM modulation remain unclear.

METHODS: In this study, 8-week-old rats were assigned to three groups after a two-week acclimation: C (normal diet for six weeks), M (adenine diet for four weeks then normal diet for two weeks), and T (same as M, with JPYSF administered during the final three weeks). Fecal samples were collected at three timepoints (T1: post-acclimation; T2: after three weeks on respective diets; T3: after three weeks of JPYSF treatment) for metagenomic sequencing. Serum creatinine (SCR) was measured at T2 and T3.

RESULTS: At T2, adenine-fed rats showed elevated SCR (C: 28.4 ± 1.5 µmol/L; M: 189.6 ± 25.8µmol/L; T: 186.4 ± 32.5µmol/L; p < 0.001). By T3, SCR decreased more in T (86.0 ± 14.9µmol/L) than in M (119.6 ± 16.3µmol/L; p = 0.012), with C remaining stable (30.8 ± 4.4µmol/L). Adenine feeding induced significant GM shifts, evidenced by increased Aitchison distance (p < 0.01) and altered co-abundance interaction groups (CIGs): CIG3, 6, 9, 10 increased; CIG1, 2, 4, 12 decreased (all p < 0.05). After JPYSF treatment, only CIG4 significantly rebounded (T3 vs. M, p = 0.0079), and T3-T1 dissimilarity was lower in T than M (p < 0.05). SCR levels were significantly lower in T than M after returning to a normal diet, suggesting a renoprotective effect of JPYSF. Co-occurrence analysis linked SCR positively with toxin-associated CIGs (CIG3, 6, 7, 9, 10) and pathways (purine metabolism, toluene degradation), and negatively with CIG4.

DISCUSSION: These results demonstrate that JPYSF lowers SCR and selectively modulates GM modules, particularly CIG4, which inversely correlates with uremic toxin-producing pathways, suggesting improved renal function and specific gut microbiota modulation in CKD rats.}, } @article {pmid40702703, year = {2025}, author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M}, title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40702703}, issn = {1477-4054}, support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; }, abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.}, } @article {pmid40701508, year = {2025}, author = {Chen, WJ and Wang, JP and Zhou, JR and He, Y and An, DQ and Tian, TT and Liang, MT and Aikepa, D and Kahaer, M and Sun, YP}, title = {Efficacy and mechanisms of compound Bai Mao Yin in regulating uric acid transport and improving the intestinal microbiota to alleviate hyperuricemia via the enterorenal axis.}, journal = {Microbial pathogenesis}, volume = {207}, number = {}, pages = {107922}, doi = {10.1016/j.micpath.2025.107922}, pmid = {40701508}, issn = {1096-1208}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Uric Acid/metabolism/blood ; Mice ; *Hyperuricemia/drug therapy/metabolism/microbiology ; Male ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Middle Aged ; Feces/microbiology ; Female ; Metagenomics ; Kidney/metabolism/drug effects ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/drug effects ; Biological Transport/drug effects ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: The compound Bai Mao Yin (BMY) has demonstrated therapeutic efficacy in reducing uric acid (UA) levels; however, its underlying mechanisms remain unclear.

METHODS: The UA-lowering effects of BMY were evaluated in a cohort of 40 patients with hyperuricemia (HUA) who received BMY treatment for 90 days. Fecal samples were collected at baseline (day 0), mid-treatment (day 30), and post-treatment (day 90) for metagenomic sequencing to analyze changes in gut microbiota and identify potential BMY targets in HUA. These clinical findings were validated in a hyperuricemic mouse model induced by xanthine and potassium oxonate. Mouse fecal samples were analyzed via 16S rDNA (V3-V4 region) sequencing to assess microbiota shifts. Additionally, fecal microbiota transplantation (FMT) from BMY-treated mice to HUA mice and in vitro cell experiments using HK2 cells were conducted to investigate the roles of BMY and the reconstructed microbiota in UA metabolism, renal UA transport, and inflammation through upstream signaling pathways.

RESULTS: Clinical cohort studies demonstrated that the BMY effectively lowers UA levels in patients with HUA without inducing hepatorenal toxicity. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of metagenomic data revealed that BMY modulates the gut microbiota and influences ATP-binding cassette transporters and UA metabolism-related pathways. In animal models, BMY increased the relative abundance of beneficial gut bacteria, reduced intestinal permeability, and regulated UA transporters in both intestinal and renal systems, contributing to UA reduction. In vitro assays showed that BMY directly decreased UA levels in the cell supernatant and suppressed interleukin-1β (IL-1β) and interleukin-6 (IL-6) expression by downregulating the TLR4/MYD88/NFκB signaling pathway, thereby alleviating inflammation.

CONCLUSIONS: Compound BMY was found to improve the intestinal microenvironment and modulate UA transport via the enterorenal axis, effectively reducing HUA.}, } @article {pmid40700599, year = {2025}, author = {Mofidifar, S and Tefagh, M}, title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {7}, pages = {}, pmid = {40700599}, issn = {1367-4811}, mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; }, abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.

RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.

PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.}, } @article {pmid40697984, year = {2025}, author = {Hebbar, P and Han, OB and Yan, NX and Kay, D and Chu, KY and Woon, JS and Lun, PK and Kabekkodu, SP and Prasad, ASB and Prakash, B and Nograles, N and Kanakal, MM and Goodson, M and Nagaraja, S and Mascarenhas, R}, title = {Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia.}, journal = {Access microbiology}, volume = {7}, number = {6}, pages = {}, pmid = {40697984}, issn = {2516-8290}, abstract = {The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed Pseudomonadota (67-69%), Bacteroidota (6-8%), Bacillota (5-8%), Campylobacterota (4-5%), Acidobacteriota (3-4%), Planctomycetota (2-4%) and Actinomycetota (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of Burkholderiaceae, Bacillaceae and Enterobacteriaceae suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.}, } @article {pmid40696437, year = {2025}, author = {Ashton, PM and Mageiros, L and Meiring, JE and Chunga-Chirambo, A and Khanam, F and Dongol, S and Banda, H and Karkey, A and Preciado-Llanes, L and Thomaides-Brears, H and Gibani, M and Rajib, NH and Rahman, N and Biswas, PK and Bhuiyan, MAI and Kay, S and Auger, K and Seret, O and Thomson, NR and Pollard, AJ and Baker, S and Basnyat, B and Clemens, JD and Dolecek, C and Dunstan, SJ and Dougan, G and Heyderman, RS and Pitzer, VE and Qadri, F and Gordon, MA and Holt, KE and Darton, TC and , }, title = {Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {168}, pmid = {40696437}, issn = {2049-2618}, mesh = {Humans ; *Typhoid Fever/microbiology/epidemiology ; *Gastrointestinal Microbiome ; *Salmonella typhi/pathogenicity ; Prospective Studies ; Male ; Female ; Malawi/epidemiology ; Adult ; Bangladesh/epidemiology ; Nepal/epidemiology ; Adolescent ; Child ; Feces/microbiology ; Young Adult ; Endemic Diseases ; Fatty Acids, Volatile/metabolism ; Middle Aged ; Child, Preschool ; }, abstract = {BACKGROUND: Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and water, particularly in settings with poor water and sanitation infrastructure, resulting in over 10 million illnesses annually. As the pathogen invades via the gastrointestinal tract, it is plausible that the gut microbiome may influence the outcome of S. Typhi exposure. There is some evidence that bacteria producing short-chain fatty acids (SCFAs) may create an environment unfavourable to invasive Salmonella, but data from humans is limited.

METHODS: To investigate the association between the gut microbiome and typhoid fever, we analysed samples collected from three all-age cohorts enrolled in a prospective surveillance study conducted across three settings where typhoid fever is endemic (Dhaka, Bangladesh; Blantyre, Malawi; and Kathmandu, Nepal). Cohorts consisted of acute typhoid fever patients (n = 92), asymptomatic household contacts of typhoid fever patients (representing individuals who were likely exposed to S. Typhi but did not develop the disease, n = 97) and asymptomatic serosurvey participants with high Vi antibody titres (representing individuals who were exposed to S. Typhi and may be carriers, n = 69). The stool microbiomes of each cohort were characterised using shotgun metagenomics, and bacterial diversity, composition and function were compared.

RESULTS: We identified 4 bacterial species that were significantly lower in abundance in typhoid fever patients compared with household contacts (i.e. probably exposed), in two of the three participant populations (Bangladesh and Malawi). These bacteria may represent taxa that provide protection against the development of clinical infection upon exposure to S. Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. The putative protection provided by microbiome SCFA metabolism was supported by data from a controlled human infection model conducted in a UK population, in which participants who did not develop typhoid fever following ingestion of S. Typhi had a higher abundance of a putative SCFA-metabolising MGC (q-value = 0.22).

CONCLUSIONS: This study identified the same protective associations between taxonomic and functional microbiota characteristics and non-susceptibility to typhoid fever across multiple human populations. Future research should explore the potential functional role of SCFAs and inflammation-associated bacteria in resistance to S. Typhi and other enteric infections. Video Abstract.}, } @article {pmid40695901, year = {2025}, author = {Awad, N and Larson, PJ and Sissoko, CA and Bond, LL and Dion, GR}, title = {Metagenomic whole genome shotgun analysis of the airway microbiome in laryngotracheal stenosis: a pilot study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {26570}, pmid = {40695901}, issn = {2045-2322}, mesh = {Humans ; Pilot Projects ; *Microbiota/genetics ; *Laryngostenosis/microbiology ; *Tracheal Stenosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Metagenome ; Adult ; Tracheostomy ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; }, abstract = {The airway microbiome has been implicated in the pathogenesis of laryngotracheal stenosis (LTS), yet prior studies using 16 S rRNA sequencing have limited sub-genus level resolution. Metagenomic whole genome shotgun sequencing (mWGS) allows for strain-level taxonomic and functional genomic analysis, providing detailed insights into specific organisms and pathways. A pilot study was conducted to explore the advantages and challenges of mWGS in investigating the airway metagenome in LTS. mWGS was conducted on 12 intraoperative swab samples from 8 LTS patients, divided into tracheostomy-dependent (n = 3) and non-tracheostomy (n = 5) groups, and 4 controls. Patient comorbidities, antibiotic use, and medications were documented. Biobakery workflows were used for taxonomic and functional profiling. Species-specific reference databases were constructed for 6 abundant species for strain-level analyses. LTS samples had decreased taxonomic diversity and were dominated by species with previously described roles in other chronic inflammatory processes such as Staphylococcus aureus, Streptococcus parasanguinis, Streptococcus mitis, and Corynebacterium pseudogenitalium. LTS samples were enriched for pathways involved in fatty acid biosynthesis and formaldehyde metabolism. Our results identified tracheostomy as an important potential confounder in airway metagenomics but show mWGS techniques are promising in uncovering microbiota correlates in LTS that could reveal disease-specific biomarkers, comorbidity links, and therapeutic targets.}, } @article {pmid40692682, year = {2025}, author = {Qin, X and Xi, L and Zhao, L and Han, J and Qu, H and Xu, Y and Weng, W}, title = {Exploring the distinctive characteristics of gut microbiota across different horse breeds and ages using metataxonomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1590839}, pmid = {40692682}, issn = {2235-2988}, mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Age Factors ; Metagenomics/methods ; DNA, Bacterial/genetics ; Biodiversity ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Gut microbiota exerts a pivotal function in host nutrient metabolism and maturation of the mucosal immunity. Analyzing the reciprocal interaction between horses and gut microbiota constitutes a crucial aspect of scientific feeding practices. This study aims to investigate the differences in gut microbiota among Hequ horses, Mongolian horses, and Thoroughbred horses, as well as between Thoroughbred horses at two age stages.

METHODS AND RESULTS: Paired-end sequencing with a read length of 2×250 bp targeting the V3-V4 region of the 16S rRNA gene in fecal samples was carried out. Subsequently, differences in the diversity, composition, and metabolic pathways of the gut microbiota among the groups were analyzed. The results showed that: (1) Horse breeds were associated with variations in the gut microbiota. Microbial diversity, the proportion of commensal bacteria from Bacillota and Bacteroidota, and bacterial communities involved in dietary fiber metabolisms were significantly higher in the gut of the Hequ horses than in the gut of the Mongolian and Thoroughbred horses. The highest Bacillota to Bacteroidota (B/B) ratio and enrichment of bacterial communities involved in the metabolism of bile acids, lipids, and amino acids in the gut of the Mongolian horses resulted in significantly higher lipid metabolism and amino acid metabolism than in the other two breeds. The bacterial communities enriched in the gut of Thoroughbred horses were primarily involved in carbohydrate metabolism, but the level of energy metabolism was significantly lower than in Hequ horses. (2) The results also showed an association between age and gut microbiota of Thoroughbred horses. The alpha diversity, B/B ratio, and 83.33% of metabolic pathways did not differ significantly between younger and older Thoroughbred horses. However, there were significant differences between the two age groups in beta diversity, composition of glycolytic bacteria, metabolism of cofactors and vitamins, and energy metabolism of gut microbiota.

CONCLUSIONS: Collectively, these results point to an association between the breed of horses or the age of Thoroughbred horses with variations in gut microbiota. The current findings will serve as a reference for improving feeding strategies for horses.}, } @article {pmid40692127, year = {2025}, author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Moon, JK and Jain, A}, title = {Distribution of Surface-Layer Prokaryotes in the Western Arctic Ocean: Responses to Pacific Water Inflow and Sea Ice Melting.}, journal = {Environmental microbiology}, volume = {27}, number = {7}, pages = {e70154}, doi = {10.1111/1462-2920.70154}, pmid = {40692127}, issn = {1462-2920}, support = {//National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Govt. of India/ ; //Korea Polar Research Institute/ ; //The Ministry of Oceans and Fisheries, Republic of Korea/ ; }, mesh = {Arctic Regions ; *Ice Cover/microbiology ; *Archaea/genetics/classification/isolation & purification ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pacific Ocean ; Microbiota ; Metagenome ; }, abstract = {Here, we evaluated how microbial community composition and functions vary along the path of Pacific water inflow, starting from the Bering Sea via the Chukchi Sea to the central Arctic Ocean. Our findings reveal that the inflow of Pacific water and sea ice melt significantly influence the environmental settings of the western Arctic Ocean, resulting in distinct prokaryotic communities with varied distribution patterns between the open Chukchi Sea and the Ice-covered central Arctic Ocean. The heterotrophic populations reliant on phytoplankton predominated in the Bering Sea and Southern Chukchi Sea, while in the Central Arctic Ocean, chemoautotrophic bacteria and archaea contributed equally with heterotrophic populations adapted to oligotrophic conditions. Although no specific functional genes were universally enriched across the metagenome libraries of prokaryotic communities, the relative abundance of functional genes varied among oceanic sectors. The assembly processes of prokaryotic communities in the western Arctic Ocean were found to be influenced by both deterministic and stochastic factors, with deterministic processes playing a more significant role. Thus, the ongoing increases in Pacific inflow and sea ice melt could lead to the displacement of native chemoautotrophic and oligotrophic populations in the Arctic Ocean by fast-growing heterotrophic populations better adapted to elevated nutrient concentrations and temperatures.}, } @article {pmid40691525, year = {2025}, author = {Abdelkader, A and Ferdous, NA and El-Hadidi, M and Burzykowski, T and Mysara, M}, title = {metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {189}, pmid = {40691525}, issn = {1471-2105}, mesh = {Longitudinal Studies ; *Microbiota/genetics ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Humans ; Metagenome ; }, abstract = {BACKGROUND: Detecting biomarkers is a key objective in microbiome research, often done through 16S rRNA amplicon sequencing or shotgun metagenomic analysis. A critical step in this process is differential abundance (DA) analysis, which aims to pinpoint taxa whose abundance significantly differs between groups. However, DA analysis remains challenging due to high dimensionality, compositionality, sparsity, inter-taxa correlations, uneven abundance distributions, and missing values-all which hinder our ability to model the data accurately. Despite the availability of many DA tools, balancing high statistical power with effective false discovery rate (FDR) control remains a major limitation.

RESULTS: Here, we introduce a novel approach for DA analysis that integrates counts adjusted with Trimmed Mean of M-values (CTF) normalization and Centered Log Ratio (CLR) transformation with Generalized Estimating Equation (GEE) model. We benchmarked our approach against eight widely used tools employing both simulated and real datasets in cross-sectional and longitudinal settings. While several tools (e.g. MetagenomeSeq, edgeR, DESeq2 and Lefse) achieved high sensitivity, they often failed to adequately control the FDR. In contrast, our method demonstrated high sensitivity and specificity when compared to other approaches that successfully controlled the FDR, including ALDEx2, limma-voom, ANCOM, and ANCOM-BC2.

CONCLUSIONS: Our approach effectively addresses key challenges in microbiome data analysis across both cross-sectional and longitudinal designs. Integrated into the R package metaGEENOME (https://github.com/M-Mysara/metaGEENOME), our framework provides a flexible, scalable and statistically robust solution for DA analysis, offering improved FDR control and enhanced performance for biomarker discovery in microbiome studies.}, } @article {pmid40691449, year = {2025}, author = {Vázquez-Castellanos, JF and Maciel, LF and Wauters, L and Gregory, A and Van Oudenhove, L and Geboers, K and Verbeke, K and Smokvina, T and Tack, J and Vanuytsel, T and Derrien, M and Raes, J}, title = {Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {140}, pmid = {40691449}, issn = {2055-5008}, mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Stress, Psychological/microbiology ; *Students/psychology ; Male ; Female ; *Lacticaseibacillus rhamnosus/physiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Adult ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Anxiety ; Metagenomics ; }, abstract = {Probiotics have been widely tested for their effect on mental well-being, albeit with heterogeneous outcomes. Direct and indirect effects through the gut microbiome might lie at the basis of these observations. Here, in a post-hoc analysis, we assessed the effect of 4-week consumption of a probiotic candidate strain on the gut microbiome in students exposed to academic stress. Healthy students were randomized to consume a fermented milk product with Lacticaseibacillus rhamnosus CNCM I-3690 (N = 39) or an acidified non-fermented milk product (N = 40) twice daily for 4 weeks before academic exams. The gut microbiome was analysed by Quantitative Microbiome Profiling based on 16S rRNA gene amplicon and shotgun metagenomic sequencing. Stress and anxiety were assessed using both objective and self-reported markers. Changes of alpha-diversity markers and community shifts from baseline (beta diversity) were lower in L. rhamnosus treated individuals over controls, suggesting lower overall changes of gut microbiota during psychological stress in the Probiotic group. The intake of L. rhamnosus CNCM I-3690 induced differential abundance of some species, such as the maintenance of the quantitative abundance of Ruminococcus bicirculans, and co-varied with species, which differed according to visits (i.e., stress level), suggesting a potential beneficial effect of the strain before the highest increase of stress level. The higher quantitative abundance of F. prausnitzii induced by the probiotic intake was associated with lowered self-reported anxiety levels before the exam. Functional analysis revealed minor changes upon intake of the probiotic strain. Taken together, using a quantitative framework, we found that L. rhamnosus CNCM I-3690 has a potential effect on gut microbiome response to stress, although further studies are needed to better understand the precise interaction.}, } @article {pmid40691217, year = {2025}, author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H}, title = {Theabrownin combined with zearalenone suppresses colitis-associated colorectal cancer by inhibiting PI3K/AKT pathway and enhancing microbial propionate production.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {26386}, pmid = {40691217}, issn = {2045-2322}, mesh = {*Zearalenone/pharmacology/administration & dosage ; Animals ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; *Propionates/metabolism ; Signal Transduction/drug effects ; *Colorectal Neoplasms/drug therapy/etiology ; *Colitis-Associated Neoplasms/drug therapy/metabolism/pathology ; Male ; Cytokines/metabolism ; Fluorouracil/pharmacology ; *Colitis/complications ; Mice, Inbred C57BL ; }, abstract = {Colorectal cancer (CRC) is both a leading cause of cancer-related mortality and one of the most frequently diagnosed cancers. Previous studies have shown that zearalenone and theabrownin each exert anti-CRC effects. Here, we aimed to evaluate the anti-tumor properties of theabrownin and zearalenone mixture (TZ) and to assess whether supplementing TZ with 5-FU, a commonly used chemotherapeutic drug, could further suppress CRC tumorigenesis. Our results revealed that TZ significantly attenuated AOM/DSS-induced colorectal tumorigenesis. TZ improved survival rate, reduced tumor count, preserved colon length, and mitigated colonic inflammation in AOM/DSS mice. In addition, the concentration of pro-inflammatory cytokines IL-6, TNF-α and IL-17 A/F and proliferative PI3K/AKT were significantly reduced. Metagenomic analyses revealed that TZ modulated the gut microbiota and mycobiota composition and increased the fecal acetate and propionate levels. Furthermore, the enrichment of the bacterial Desulfovibrionaceae bacterium LT0009, Helicobacter sp. MIT 03-1616 and fungal Xylariaceae sp. FL0594 was associated with the reduction of tumor multiplicity and pro-inflammatory cytokines. No additional benefits were observed with combining TZ with 5-FU. Taken together, TZ presented remarkable inhibitory effects on colorectal tumorigenesis, indicating its potential as a novel therapeutic candidate for CRC.}, } @article {pmid40686474, year = {2025}, author = {Lledós, M and Prats-Sánchez, L and Muiño, E and Cullell, N and Llucià-Carol, L and Cárcel-Márquez, J and Gallego-Fabrega, C and Martín-Campos, JM and Marín, R and Aguilera-Simón, A and Guasch-Jiménez, M and Ezcurra-Díaz, G and Camps-Renom, P and Del Mar Freijo, M and Martí-Fàbregas, J and Fernández-Cadenas, I}, title = {Influence of the Gut Microbiota on Acute Ischemic Stroke Functional Outcomes at Three Months.}, journal = {European journal of neurology}, volume = {32}, number = {7}, pages = {e70265}, pmid = {40686474}, issn = {1468-1331}, support = {RD21/0006/0006//RICORS-ICTUS/ ; AC19/00106//ERA-Net NEURON/ ; CD20/00043//Instituto de Salud Carlos III/ ; FI19/00309//Instituto de Salud Carlos III/ ; PI18/01338//Instituto de Salud Carlos III/ ; PI20/00925//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Ischemic Stroke/microbiology/physiopathology ; Male ; Female ; Aged ; Middle Aged ; *Recovery of Function/physiology ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: Functional recovery from ischemic stroke (IS), the main cause of adult disability worldwide, is influenced by many factors, and a portion of interindividual variability remains unexplained.

METHODS: Observational study in a tertiary stroke centre of patients with IS analyzed using shotgun metagenomic sequencing (January 2020-March 2022). Functional outcomes were assessed according to modified Rankin Scale (mRS) scores 3-months post-IS, considering 0-2 favorable and 3-6 unfavorable. The causal relationship between several bacteria and post-IS outcomes was explored via two-sample Mendelian randomization (MR) analyses using Genome-Wide Association Analysis (GWAS) summary statistics.

RESULTS: Comparing 128 patients with favorable and unfavorable post-IS functional outcomes, β-diversity analysis showed a separation in microbial structure, and α-diversity measures revealed greater bacterial richness in the favorable outcomes group. Taxonomic profiling of the samples showed that a greater abundance of pathogenic bacteria (e.g., Pseudomonas, Finegoldia, Porphyromonas) was associated with an unfavorable outcome. Functional profiling of the samples revealed differences in the ethylbenzene degradation pathway and in 16S rRNA (uracil1498-N3)-methyltransferase. MR confirmed increased pyruvate levels to be causally associated with post-IS favorable outcomes (β = -0.50, 95% CI: -0.91, -0.10).

CONCLUSIONS: Our study points to gut microbiota differences in patients with unfavorable versus favorable 3-month post-IS outcomes. Patients with unfavorable outcomes presented gut microbiota dysbiosis and alterations in multiple metabolic pathways.

TRIAL REGISTRATION: This study was registered on 3 October 2021 with https://clinicaltrials.gov. Access number: NCT04795687.}, } @article {pmid40685922, year = {2025}, author = {Chen, QY and Shao, MM and Dong, SF and Shi, HZ and Yi, FS}, title = {Metagenomic and Metabolomic Profiling Reveals the Impact of High-Fat Diet on Malignant Pleural Effusion.}, journal = {Thoracic cancer}, volume = {16}, number = {14}, pages = {e70126}, pmid = {40685922}, issn = {1759-7714}, support = {7232066//Natural Science Foundation of Beijing Municipality/ ; 82200111//National Natural Science Foundation of China/ ; 048//Beijing Scholars Program/ ; QML20230303//Beijing Hospitals Authority Youth Program/ ; Ggyfz202314//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ggyfz202330//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ggyfz202416//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; }, mesh = {Animals ; Mice ; *Diet, High-Fat/adverse effects ; *Metabolomics/methods ; *Metagenomics/methods ; *Pleural Effusion, Malignant/etiology/metabolism/pathology ; Male ; Gastrointestinal Microbiome ; Humans ; *Metabolome ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Malignant pleural effusion (MPE) is a common complication in the advanced stage of cancer. High-Fat Diet (HFD)-induced obesity has become a common metabolic background in cancer patients. Recent studies have demonstrated that HFD induces gut dysbiosis, resulting in alterations in metabolites and immune responses. However, its role in MPE remains unclear.

METHODS: We established an MPE mouse model under both normal chow and HFD conditions. Metagenomic sequencing of fecal samples and untargeted metabolomics of plasma were performed to assess alterations in gut microbiota and systemic metabolites, respectively. Bioinformatic and statistical analyses were conducted to identify significant microbial taxa and metabolic pathways.

RESULTS: HFD-fed mice exhibited increased pleural effusion. Metagenome data of the intestinal microbiome and metabolome profiles of plasma metabolites revealed key taxa-Akkermansiaceae, Parabacteroides, and Muribaculaceae-as well as significant metabolic pathways involved in sphingolipid metabolism, glycerophospholipid metabolism, and steroid hormone biosynthesis.

CONCLUSION: These findings suggest that HFD may accelerate the MPE progression through modulation of gut microbiota and plasma metabolites, providing new strategies for prevention and treatment.}, } @article {pmid40685618, year = {2025}, author = {Morsy, Y and Walberg, Å and Wawrzyniak, P and Hubeli, B and Truscello, L and Mamie, C and Niechcial, A and Gueguen, E and Manzini, R and Gottier, C and Lang, S and Scharl, S and Blümel, S and Biedermann, L and Rogler, G and Turina, M and Ramser, M and Petrowsky, H and Arnold, IC and Zeissig, S and Zamboni, N and Egli, A and Niess, JH and Hruz, P and Knuth, A and Fritsch, R and Manz, MG and Wawrzyniak, M and Scharl, M}, title = {Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2530157}, pmid = {40685618}, issn = {1949-0984}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/immunology/blood ; *Inflammatory Bowel Diseases/microbiology/immunology/blood ; *Leukocytes, Mononuclear/microbiology/immunology ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; Metagenomics ; Adult ; Bacterial Translocation ; Aged ; }, abstract = {The involvement of the intestinal microbiome in the pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC), is well-established. Bacteria interact with immune cells at sites of intestinal inflammation, but also in the CRC tumor microenvironment. We hypothesized that bacterial remnants translocate within peripheral blood mononuclear cells (PBMCs) into the circulation and thus explored the composition of the detectable microbiome in PBMCs of patients with CRC or IBD compared to healthy controls. The PBMC microbiome profiles partially align with the tumor-derived or intestinal tissue-derived microbiome signatures obtained from the same patients with CRC or IBD, respectively. Our metagenomics data, supported by 16S-rRNA-FISH-Flow, imaging flow cytometry and species-specific qPCR, revealed the presence of translocated bacterial genetic sequences in the patients with CRC and IBD. Thus, our data suggest that in patients with intestinal barrier leakage, there is the potential for the translocation of bacterial remnants into the circulation via PBMCs.}, } @article {pmid40684088, year = {2025}, author = {Kreisinger, J and Kaňková, Š and Dlouhá, D and Ullmann, J and Nouzová, K and Hrbáčková, H and Schmiedová, L and Takács, L}, title = {Associations between psychological or biological stress indicators and gut microbiota in pregnant women - findings from a prospective longitudinal study.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {442}, pmid = {40684088}, issn = {1471-2180}, support = {21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; 21-23288S//Grantová Agentura České Republiky,Czechia/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Prospective Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; Anxiety/microbiology ; *Stress, Psychological/microbiology ; Depression/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Hydrocortisone/blood ; Young Adult ; Surveys and Questionnaires ; Pregnant People/psychology ; Postpartum Period ; }, abstract = {BACKGROUND: The perinatal period has been linked with higher vulnerability to stress and symptoms of depression and anxiety, as well as with dynamic changes in the composition of maternal gut microbiota. While recent studies indicated significant associations between stress, depression, or anxiety, and alterations in gut microbiota in pregnant women, research in this avenue is still emerging, with existing studies often being limited by small sample sizes.

METHOD: We conducted a prospective longitudinal study of 171 women, collecting gut microbiota samples in each trimester of pregnancy and in the early postpartum, questionnaire data (perceived stress via the Perceived Stress Scale, symptoms of depression via the Edinburgh Postnatal Depression Scale, and anxiety via the 6-item State-Trait Anxiety Inventory) twice in each trimester and twice in the early postpartum period, and blood samples for cortisol levels analysis in the first and third pregnancy trimesters. Gut microbiota samples were analyzed by amplicon sequencing of 16S rRNA gene.

RESULTS: Perceived stress and symptoms of depression and anxiety showed moderate temporal changes and a high consistency at the individual level over the study period. Cortisol levels rose significantly from the first to the third trimester. There were significant temporal changes in microbiota composition between the first and second trimesters, and between the first and third trimesters. After controlling for false positive findings due to multiple testing, we found no significant associations between stress-related variables (perceived stress, cortisol levels, symptoms of depression and anxiety) and gut microbiota diversity, microbial community composition, or relative abundances of individual bacterial taxa.

CONCLUSIONS: The present study results contradict previous research that indicated significant associations between emotions and gut microbiota in the perinatal period. Although we cannot provide an ultimate explanation for this discrepancy, we propose it can lie in insufficient control for false positives in the differential abundance analyses in most previous studies.}, } @article {pmid40683926, year = {2025}, author = {Zafeiropoulou, K and Voermans, B and Ngo, H and Moreno, J and Lee, D and Derikx, JPM and Luyer, M and Zwinderman, AH and Nieuwdorp, M and de Goffau, M and de Jonge, WJ and Levin, E}, title = {Application of image guided analyses to monitor fecal microbial composition and diversity in a human cohort.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {26237}, pmid = {40683926}, issn = {2045-2322}, support = {09150182010020//Amsterdam University Medical Centers/ ; 101141346/ERC_/European Research Council/International ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Cohort Studies ; Adult ; Smartphone ; *Bacteria/genetics/classification ; Metagenomics/methods ; Middle Aged ; }, abstract = {The critical role of gut microbiota in human health and disease has been increasingly illustrated over the past decades, with a significant amount of research demonstrating an unmet need for self-monitor of the fecal microbial composition in an easily-accessible, rapid-time manner. In this study, we employed a tool for Smartphone Microbiome Evaluation and Analysis in Rapid-time (SMEAR) that uses images of fecal smears to predict microbial compositional characteristics in a human cohort. A subset of human fecal samples was randomly retrieved from the second wave of data collection in the Healthy Life in an Urban Setting (HELIUS) study cohort. Per sample, 16S rRNA gene sequencing data was generated in addition to an image of a fecal smear, spread on a standard A4 paper. Metagenomics-paired pictures were used to validate a computer vision-based technology to classify whether the sample is of low or high relative abundance of the 50 most abundant genera, and α-diversity (Shannon-index). In total, 888 fecal samples were used as an application of the SMEAR technology. SMEAR gave accurate predictions whether a fecal sample is of low or high relative abundance of Sporobacter, Oscillibacter and Intestinimonas (very good performance, AUC > 0.8, p-value < 0.001, for all models), as well as Neglecta, Megasphaera, Lachnospira, Methanobrevibacter, Harryflintia, Roseburia, and Dialister (good performance, AUC > 0.75, p-value < 0.001, for all models). Likewise, SMEAR could classify whether a fecal sample was of low or high α-diversity (AUC = 0.83, p-value < 0.001). Our study demonstrates that SMEAR robustly predicts microbial composition and diversity from digital images of fecal smears in a human cohort. These findings establish SMEAR as a new benchmark for rapid, cost-effective microbiome diagnostics and pave the way for its direct application in research settings and clinical validation.}, } @article {pmid40683886, year = {2025}, author = {Wu, T and Guo, SZ and Zhang, Y and Zhao, XZ and Ran, CG and Liu, FL and Wang, RH and Li, DF and Zhu, HZ and Jiang, CY and Shen, XH and Liu, SJ}, title = {The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {139}, pmid = {40683886}, issn = {2055-5008}, support = {41991333//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 32270084//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; }, mesh = {Biodegradation, Environmental ; *Polybrominated Biphenyls/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil Microbiology ; Metagenomics ; Soil Pollutants/metabolism ; }, abstract = {The capability to understand and construct synthetic microbiomes is crucial in biotechnological innovation and application. Tetrabromobisphenol A (TBBPA) is an emerging pollutant, and the understanding of its biodegradation is very limited. Here, a top-down approach was applied for the enrichment of TBBPA-degrading microbiomes from natural microbiomes. Ten keystone taxa correlated to TBBPA degradation and their co-occurrence interactions were identified by the dissection of the degrading microbiomes. Those keystone taxa were targeted and cultivated, and the genomic information was obtained by genome sequencing of strains and metagenomic binning. The keystone bacterial strains showed efficient degradation of TBBPA, and L-amino acids were important co-metabolic substrates to promote the degradation. Guided by this knowledge, a bottom-up approach was applied to design and construct a simplified synthetic consortium SynCon2, that consisted of four strains. The SynCon2 demonstrated efficient TBBPA degradation activity and soil bioremediation. Our study demonstrates the importance of the application of multiple tools in understanding the functions of microbiomes and provides an integrated top-down and bottom-up strategy for the construction of synthetic microbiomes with various applications.}, } @article {pmid40681522, year = {2025}, author = {Xiang, X and Li, Y and Ye, J and Li, B and He, G and Zhu, M and Zhang, J and Zhang, B and Miao, M and Yang, Y}, title = {Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {136}, pmid = {40681522}, issn = {2055-5008}, support = {Z191100008619006//Beijing Municipal Science and Technology Commission/ ; CASNHP-MJN2023-04//the Chinese Association for Student Nutrition & Health Promotion-Mead Johnson Nutritionals (China) Joint Fund/ ; 21JZD039//Major Research Project on Philosophy and Social Sciences of the Ministry of Education/ ; 2021YFC2600501//National Key R&D Program Project of the Ministry of Science and Technology/ ; }, mesh = {*Bacteria/genetics/classification/isolation & purification ; China ; Fermentation ; *Fermented Foods/microbiology ; Food Microbiology ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Glycine max/microbiology ; *Metagenomics/methods ; *Microbiota ; *Soy Foods/microbiology ; Humans ; }, abstract = {Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotgun metagenomics, we examined microbiota of 93 representative samples spanning three major categories of traditional Chinese fermented soybean products. We identified distinct microbial and functional profiles across food types, with antagonism between beneficial taxa (Bacillales and Lactobacillales) and harmful Enterobacterales. Comparative analysis with public Chinese gut microbiomes revealed species- and strain-sharing between fermented foods and human gut microbiota, identifying certain products as sources of clinically relevant pathogens, including Klebsiella pneumoniae and Klebsiella quasipneumoniae. Horizontal gene transfer analysis highlighted potential transfer of ARGs (e.g., efflux pump genes) from food microbes to gut microbiota. Our findings underscore the need to integrate microbial surveillance into traditional fermentation to balance health benefits with food safety.}, } @article {pmid40680146, year = {2025}, author = {Li, B and Sakaguchi, T and Tani, H and Ito, T and Murakami, M and Okumura, R and Kobayashi, M and Okuzaki, D and Motooka, D and Ikeuchi, H and Ogino, T and Mizushima, T and Hirota, S and Otake-Kasamoto, Y and Kishikawa, T and Nakamura, S and Kobiyama, K and Ishii, KJ and Hashiguchi, T and Kawai, T and Kuroda, E and Shinzaki, S and Ise, W and Kurosaki, T and Kikuchi, A and Tomofuji, Y and Okada, Y and Takeda, K and Kayama, H}, title = {OTUD3 prevents ulcerative colitis by inhibiting microbiota-mediated STING activation.}, journal = {Science immunology}, volume = {10}, number = {109}, pages = {eadm6843}, doi = {10.1126/sciimmunol.adm6843}, pmid = {40680146}, issn = {2470-9468}, mesh = {Animals ; *Colitis, Ulcerative/immunology/microbiology/prevention & control/genetics/pathology ; Mice ; Humans ; *Membrane Proteins/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; Mice, Inbred C57BL ; Fibroblasts/metabolism/immunology ; Male ; Female ; Nucleotides, Cyclic/metabolism ; Mice, Knockout ; }, abstract = {Ulcerative colitis (UC) develops through a complicated interaction between the host and microbiota. Intestinal fibroblasts are believed to play crucial roles in the pathogenesis of UC, but the influence of the host-microbiota interaction on the pathophysiology of intestinal fibroblasts remains poorly understood. Here, we demonstrate that OTU deubiquitinase 3 (OTUD3) suppresses pathologic activation of fibroblasts exposed to microbial cyclic GMP-AMP (3'3'-cGAMP) in the colon by deubiquitinating stimulator of interferon genes (STING). Mice harboring a UC risk missense variant in the Otud3 gene showed pathological features of UC in the colon after transplantation of a fecal microbiota with the potential to produce excessive cGAMP from patients with UC. Collectively, these results highlight a mechanism of the interaction between OTUD3 in host fibroblasts and STING-activating microbiota in UC development.}, } @article {pmid40679638, year = {2025}, author = {Fulke, AB and Sharma, N and Nadekar, J}, title = {Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {77}, pmid = {40679638}, issn = {1432-184X}, support = {OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; }, mesh = {*Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Microbiota ; *Biodiversity ; Metagenomics/methods ; Ecosystem ; Hydrothermal Vents/microbiology ; Oceans and Seas ; }, abstract = {Microorganisms are essential players in Earth's ecosystems, demonstrating remarkable adaptability to harsh conditions including arctic ice caps, deep-sea hydrothermal vents, and high-pressure oceanic zones. While the study of these extremophiles has long been constrained by challenges in culturing, recent advances in metagenomic techniques have enabled a deeper understanding of microbial diversity in these extreme habitats. This review explores both culturable and non-culturable microbial communities, focusing on the diverse strategies employed by microorganisms to thrive in harsh conditions, including high pressure, temperature, salinity, and nutrient limitations. Traditional cultivation methods often fail to capture the full spectrum of deep-sea microbiota due to the unique growth requirements of many organisms. In the omic era, however, microbial cultivation and the function of microbial resources are important. Non-culturable methods, like metagenomic studies and environmental DNA sequencing, have uncovered hitherto unknown microbial taxa and metabolic pathways, offering important new information on microbial ecology and biogeochemistry. The complex microbial interactions and adaptive methods that support these ecosystems are highlighted by case studies, including as studies on hydrothermal plumes and hadal deposits. The expanding significance of non-culturable techniques in microbial research is highlighted in this review, which also highlights how they might help us better understand microbial life in harsh conditions and how they may be used in biotechnology and environmental management.}, } @article {pmid40678348, year = {2025}, author = {Köhler, M and Castro Sánchez-Bermejo, P and Hähn, G and Ferlian, O and Eisenhauer, N and Wubet, T and Haider, S and Bruelheide, H}, title = {Foliar Endophytic Fungal Communities Are Driven by Leaf Traits-Evidence From a Temperate Tree Diversity Experiment.}, journal = {Ecology and evolution}, volume = {15}, number = {7}, pages = {e71691}, pmid = {40678348}, issn = {2045-7758}, abstract = {Fungal endophyte communities are mainly driven by host plant identity and geographic location. However, little is known about interactions between endophytes and characteristics of the host plant such as leaf functional traits, which vary both among and within host species. Previous studies focused on a limited number of host plant species and did not control for varying conditions in the host's neighborhood, which affect leaf functional traits and, in turn, might affect fungal endophyte communities. Using a tree diversity experiment in which all trees grow under standardized conditions, we were able to assess the contributions of host tree identity, host neighborhood species richness, and host community composition as well as the variation of leaf traits caused by these factors on taxonomic richness and community composition of foliar fungal endophytes. We used next-generation amplicon sequencing to analyze the fungal endophyte community and visible-near infrared spectrometry data to predict the mean values and the intra-individual variation of leaf traits in individual trees. We found both mean trait values and intra-individual trait variation to have significant effects on endophyte richness. Mean trait values of leaf dry matter content, leaf carbon, leaf nitrogen, and leaf carbon-to-nitrogen ratio exhibited negative effects on endophyte richness, whereas specific leaf area and leaf phosphorus content increased endophyte richness. Additionally, intra-individual leaf-trait variation generally had positive effects on richness. Overall endophyte community composition was influenced by mean leaf dry matter content and specific leaf area. Ascomycota were influenced by the specific leaf area, whereas Basidiomycota responded to leaf dry matter content. We demonstrate that functional leaf traits affect foliar endophyte communities, with positive diversity effects of host leaf nutrients that are essential, and likely limiting, for fungal endophytes. Although our study emphasizes the role of leaf traits in shaping fungal communities, we also acknowledge that these dynamic interactions could lead to traits being influenced by microbes through microbe-plant interactions.}, } @article {pmid40677913, year = {2025}, author = {Piro, VC and Reinert, K}, title = {ganon2: up-to-date and scalable metagenomics analysis.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {3}, pages = {lqaf094}, pmid = {40677913}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; *Software ; Humans ; Microbiota/genetics ; Algorithms ; }, abstract = {The fast growth of public genomic sequence repositories greatly contributes to the success of metagenomics. However, they are growing at a faster pace than the computational resources to use them. This challenges current methods, which struggle to take full advantage of massive and fast data generation. We propose a generational leap in performance and usability with ganon2, a sequence classification method that performs taxonomic binning and profiling for metagenomics analysis. It indexes large datasets with a small memory footprint, maintaining fast, sensitive, and precise classification results. Based on the full NCBI RefSeq and its subsets, ganon2 indices are on average 50% smaller than state-of-the-art methods. Using 16 simulated samples from various studies, including the CAMI 1+2 challenge, ganon2 achieved up to 0.15 higher median F1-score in taxonomic binning. In profiling, improvements in the F1-score median are up to 0.35, keeping a balanced L1-norm error in the abundance estimation. ganon2 is one of the fastest tools evaluated and enables the use of larger, more diverse, and up-to-date reference sets in daily microbiome analysis, improving the resolution of results. The code is open-source and available with documentation at https://github.com/pirovc/ganon.}, } @article {pmid40676575, year = {2025}, author = {Wei, F and Wu, Z and Li, G and Sun, X and Shi, X and Tan, L and Ai, T and Qu, L and Zheng, S}, title = {Ensemble learning for microbiome-based caries diagnosis: multi-group modeling and biological interpretation from salivary and plaque metagenomic data.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {1188}, pmid = {40676575}, issn = {1472-6831}, mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; *Dental Plaque/microbiology ; *Saliva/microbiology ; *Microbiota/genetics ; *Machine Learning ; Child ; *Metagenomics ; Child, Preschool ; Female ; Male ; RNA, Ribosomal, 16S ; Neural Networks, Computer ; Ensemble Learning ; }, abstract = {BACKGROUND: Oral microbiota is a major etiological factor in the development of dental caries. Next-generation sequencing techniques have been widely used, generating vast amounts of data which is underexplored. The advancement of artificial intelligence (AI) technologies has made it possible to mine information from these large datasets. This study aimed to develop AI-driven diagnostic models and identify key microbial features for caries.

METHODS: We collected raw metagenomic and full-length 16 S rRNA gene sequencing data from previous studies on saliva and plaque to construct a caries AI training dataset comprising nearly 600 samples. Samples were grouped based on age, sequencing and sampling method. Through systematic comparison of seven machine learning architectures, including Logistic Regression, Random Forest, Support Vector Machines, Gradient Boosting, Convolutional Neural Networks, Feedforward Neural Networks, and Transformer models, we developed subgroup-specific caries diagnostic models, with subsequent ensemble learning integration to enhance generalizability.

RESULTS: The caries diagnostic model achieved a maximum AUC value of 1 (accuracy of 100%) for children under 6 years old in both saliva and plaque groups. The consistency of top features (species and metabolic pathways) contributing to the models was demonstrated through intra- and inter-group analyses. Key caries-associated species included Streptococcus salivarius, Streptococcus parasanguinis and Veillonella dispar. Veillonella parvula exhibits higher abundance in caries plaque samples, while being elevated in healthy saliva samples. Metabolic pathways like geranylgeranyl diphosphate and fructan biosynthesis were enriched in caries, whereas Bifidobacterium shunt and peptidoglycan biosynthesis were depleted.

CONCLUSION: The current work provided reliable diagnostic models for early childhood caries, and established a robust computational framework for AI-driven microbiome analysis. This study, by focusing on the characteristics of the oral microbiome, offers novel perspectives for data mining and validation of existing data through the application of AI modelling.}, } @article {pmid40674393, year = {2025}, author = {Mubaraki, FA}, title = {Extensive novel diversity and phenotypic associations in the dromedary camel microbiome are revealed through deep metagenomics and machine learning.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0328194}, pmid = {40674393}, issn = {1932-6203}, mesh = {*Camelus/microbiology ; Animals ; *Metagenomics/methods ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Phenotype ; *Microbiota ; }, abstract = {The dromedary camel, also known as one-humped camel or Arabian camel, is iconic and economically important to Arabian society. Its contemporary importance in commerce and transportation, along with the historical and modern use of its milk and meat products for dietary health and wellness, make it an ideal subject for scientific scrutiny. The gut microbiome has recently been associated with numerous aspects of health, diet, lifestyle, and disease in livestock and humans alike, as well as serving as an exploratory and diagnostic marker of many physical characteristics. Our initial pilot analysis of 55 camel gut microbiomes from the Fathi Camel Microbiome Project uses deep metagenomic shotgun sequencing to reveal substantial novel species-level microbial diversity, for which we have generated an extensive catalog of prokaryotic metagenome-assembled microorganisms (MAGs) as a foundational microbial reference database for future comparative analysis. Exploratory correlation analysis shows substantial correlation structure among the collected subject-level metadata, including physical characteristics. Machine learning using these novel microbial markers, as well as statistical testing, demonstrates strong predictive performance of microbial taxa to distinguish between multiple dietary and lifestyle characteristics of dromedary camels. We present strongly predictive machine learning models for camel age, diet (especially wheat intake), and level of captivity. These findings and resources represent substantial strides toward understanding the camel microbiome and pave the way for a deeper understanding of the nuanced factors that shape camel health.}, } @article {pmid40674041, year = {2025}, author = {Bisson, G and Comuzzi, C and FitzGerald, JA and Mukherjee, A and Renoldi, N and Innocente, N and Beresford, T and Mathur, H and Cotter, PD and Marino, M}, title = {Development of a bio-functional fermented soy beverage supplemented with microbial exopolysaccharides and its effect on the human gut microbiome in vitro.}, journal = {Food & function}, volume = {16}, number = {15}, pages = {6203-6212}, doi = {10.1039/d5fo01288k}, pmid = {40674041}, issn = {2042-650X}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Feces/microbiology ; *Polysaccharides, Bacterial/metabolism/pharmacology ; Prebiotics ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Glycine max/metabolism ; *Soy Foods/microbiology/analysis ; Male ; Fermented Foods/microbiology ; Leuconostoc mesenteroides/metabolism ; Adult ; }, abstract = {The gut microbiome plays a key role in modulating human health and well-being. Exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) are emerging as novel polymers that could exert a prebiotic effect via modification of this microbiome. Thus, incorporation of EPS to enhance food functionality is of interest. This study investigates the impact of a fermented soy beverage, supplemented with EPS produced by Leuconostoc mesenteroides DSA_O or DSA_F, on the faecal microbiota as assessed using an ex vivo model of the human distal colon. The soy beverage (SM) was prepared by fermentation with Lactiplantibacillus paraplantarum GB3 followed by supplementation with EPS_O (SMO) or EPS_F (SMF). Faecal samples from healthy donors were inoculated into a faecal fermentation medium with SM, SMO and SMF and incubated anaerobically at 37 °C for 24 h. After incubation, samples were subjected to shotgun metagenomic and short-chain fatty acid (SCFA) analysis. SMO and SMF were more effective than SM at enhancing the alpha diversity of the faecal microbiota after 24 h incubation. In addition, SMO promoted the growth of the health-associated species Bifidobacterium longum and Faecalibacterium prausnitzii, the latter of which is considered a next-generation probiotic. Butyrate and propionate levels were higher in faecal samples fermented with SMO and SMF than in SM. Taken together, these preliminary results indicate a potential role of EPS produced by Leuc. mesenteroides to be used as a functional food ingredient, modulating the gut microbiome as well as increasing the levels of SCFAs.}, } @article {pmid40671160, year = {2025}, author = {Wang, S and Kong, F and Zhang, X and Dai, D and Li, C and Cao, Z and Wang, Y and Wang, W and Li, S}, title = {Disruption of hindgut microbiome homeostasis promotes postpartum energy metabolism disorders in dairy ruminants by inhibiting acetate-mediated hepatic AMPK-PPARA axis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {167}, pmid = {40671160}, issn = {2049-2618}, support = {32130100//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; Cattle ; *Energy Metabolism ; *AMP-Activated Protein Kinases/metabolism ; *Liver/metabolism ; Homeostasis ; *Postpartum Period/metabolism ; *PPAR alpha/metabolism/genetics ; *Acetates/metabolism ; 3-Hydroxybutyric Acid/blood ; Ruminants/microbiology ; }, abstract = {BACKGROUND: Postpartum energy metabolism disorders pose a significant challenge to the health and productivity of dairy ruminants, yet their underlying pathogenesis remains poorly understood. The critical role of the gut microbiota in regulating host metabolic processes via the "gut-liver axis" has garnered increasing attention, but its specific mechanisms in dairy ruminant energy metabolism disorders are still unclear. This study uses dairy cows as a model and employs a large-scale case-control analysis to systematically investigate the pathophysiological basis of postpartum energy metabolism disorders through the lens of the "gut-liver axis."

RESULTS: Postpartum energy metabolism disorders in dairy cows are characterized by elevated blood β-hydroxybutyrate (BHB) and aspartate aminotransferase (AST) levels, and hepatic steatosis. A random forest model based on gut microbiota effectively predicts disease occurrence (AUC = 0.74). Multi-omics (metagenomics, metabolomics, and transcriptomics) analysis further identified key microbes, including Faecousia species (sp017465625 and sp017380435), Methanosphaera species (sp016282985), and Bifidobacterium globosum. These microbes regulate acetate concentration in the gut, which is significantly correlated with key genes in the hepatic PPAR and PI3K-AKT pathways, as well as with blood BHB levels. Primary hepatocyte culture experiments further confirmed that sodium acetate effectively inhibits hepatic fat deposition induced by mixed fatty acids through the hepatic AMPK-PPARA axis and reduces the production of BHB in the culture medium.

CONCLUSION: This study demonstrates that key gut microbes and their metabolic product (acetate) inhibit the occurrence of metabolic disorders through the hepatic AMPK-PPARA axis. These findings provide new insights and potential therapeutic targets for understanding and mitigating postpartum metabolic disorders in dairy ruminants. Video Abstract.}, } @article {pmid40670379, year = {2025}, author = {Shi, W and Lv, M and Wang, R and Saleem, M and Wang, L and Li, M and Wang, B and Lin, R and Xu, B and Yang, C and Ning, T and Zhou, B and Gao, Z}, title = {Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {134}, pmid = {40670379}, issn = {2055-5008}, support = {2024M751875//China Postdoctoral Science Foundation/ ; 42407427//National Natural Science Foundation of China/ ; 42377309//National Natural Science Foundation of China/ ; 2023YFD20014003//Shandong Provincial "811" Project of First-class Discipline Construction, the National Key R&D Program of China/ ; 2023BCF01015//Key R&D Program of Ningxia Hui Autonomous Region of China/ ; M2023-07//State Key Natural Science Foundations of China Laboratory of Microbial Technology Open Projects Fund/ ; SDAIT-16-01//Potato Innovation Program for the Chief Expert of Shandong Province/ ; 2021CXGC010804//Shandong Province Key R&D Program/ ; }, mesh = {*Solanum tuberosum/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Soil/chemistry ; }, abstract = {The assembly mechanisms of soil microbiome during plant disease progression remain incomplete. This study linked potato common scab (PCS) severity to destabilized soil microbiome dynamics in potato geocausphere soil (GS) through integrated metagenomic analysis and culture-based experiments. Across four Shandong fields, PCS-infected GS exhibited an 11.66% reduction in bacterial α-diversity (Shannon index) and elevated stochastic community assembly. Bacterial community structure explained 39.28% (GS) and 15.96% (bulk soil) of PCS variance, outperforming pathogen abundance contributions (14.39% GS, 7.33% BS). Two microbial interaction patterns emerged in GS: 1) synchronized shifts between pathogens and beneficial taxa as PCS intensified; 2) stochastic assembly governing entire communities but deterministic processes dominating specialized subgroups. These results propose a microbial stability framework connecting soil microbiome structural rules to plant disease progression, emphasizing community-level dynamics over pathogen-centric explanations.}, } @article {pmid40670173, year = {2025}, author = {Ai, S and Gao, D and Zhai, Z and Wang, S and Xue, Y and Liu, Z and Yan, X}, title = {[Effect mechanism of electroacupuncture on diabetic peripheral neuropathy in rats based on gut microbiota and metabolomics].}, journal = {Zhongguo zhen jiu = Chinese acupuncture & moxibustion}, volume = {45}, number = {7}, pages = {945-956}, doi = {10.13703/j.0255-2930.20250225-k0005}, pmid = {40670173}, issn = {0255-2930}, mesh = {Animals ; *Electroacupuncture ; Male ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/therapy/metabolism/microbiology ; Rats, Sprague-Dawley ; Rats ; Metabolomics ; Humans ; Acupuncture Points ; }, abstract = {OBJECTIVE: To explore the effect mechanism of electroacupuncture (EA) for ameliorating diabetic peripheral neuropathy (DPN) based on the analysis of gut microbiota and metabolomics.

METHODS: Thirty SPF-grade male SD rats were randomly divided into a normal group, a model group, and an EA group, with 10 rats in each one. Except in the normal group, the intraperitoneally injection with streptozotocin was used to induce diabetes mellitus model in the rest groups. In the EA group, acupuncture was delivered at bilateral "Zusanli" (ST36), "Sanyinjiao" (SP6), "Pishu" (BL20) and "Shenshu" (BL23), and electric stimulation was attached to "Zusanli" (ST36)-"Sanyinjiao" (SP6) and "Pishu" (BL20)-"Shenshu" (BL23), on the same side, with continuous wave and a frequency of 2 Hz, for 10 min in each intervention. The intervention measure of each group was delivered once every 2 days, 3 times a week, for 8 consecutive weeks. Body weight, random blood glucose (RBG), thermal withdrawal latency (TWL), and mechanical withdrawal threshold (MWT) before intervention, and in 4 and 8 weeks of intervention, separately, as well as sensory nerve conduction velocity (SCV) and motor nerve conduction velocity (MCV) of the sciatic nerve after intervention were measured. Metagenomic sequencing (MS) was used to analyze gut microbiota and screen for differential species. Liquid chromatography-mass spectrometry (LC-MS) was employed to detect the differential metabolites in plasma, and the metabolic pathway enrichment analysis was performed on the differential metabolites. Spearman correlation analysis was adopted to assess the relationship between gut microbiota and metabolomics.

RESULTS: After 4 and 8 weeks of intervention, when compared with the model group, the EA group showed the increase in body weight, TWL, MWT (P<0.01), and the decrease in RBG (P<0.01). Compared with the normal group, SCV and MCV, as well as Chao1 index were dropped in the model group (P<0.01), and those were elevated in the EA group when compared with those in the model group (P<0.01). The dominant bacterial phyla of each group were Firmicutes (F) and Bacteroidota (B), the ratio of them (F/B) in the model group was lower than that of the normal group (P<0.05), and F/B in the EA group was higher when compared with that in the model group (P<0.05). In comparison with the normal group, the relative abundance increased in Prevotella, Segatella, Prevotella-hominis and Segatella-copri (P<0.05); and it decreased in Ligilactobacillus, Eubacterium, Pseudoflavonifractor, Ligilactobacillus-murinus (P<0.05) in the model group. Compared with the model group, the relevant abundance of the above mentioned gut bacteria was all ameliorated in the EA group (P<0.05, P<0.01). Among the three groups, 120 differential metabolites were identified and enriched in 28 key metabolic pathways, such as glycerophospholipid and linoleic acid, of which, glycerophospholipid was the most significantly affected pathway in EA intervention. Spearman correlation analysis showed that 6 phosphatidylcholine metabolites were significantly positively correlated with Pseudoflavonifractor and were negatively with Prevotella, Segatella, Prevotella-hominis, Segatella-copri; 5 phosphatidylethanolamine metabolites were significantly negatively correlated with Pseudoflavonifractor and positively correlated with Prevotella, Segatella, Prevotella-hominis, Segatella-copri.

CONCLUSION: EA may regulate metabolic pathways such as glycerophospholipid, modulate specific gut microbiota such as Pseudoflavonifractor, Prevotella, and Segatella, and the co-expressed differential metabolites like phosphatidylcholine and phosphatidylethanolamine, thereby reducing blood glucose and protecting nerve function, so as to relieve the symptoms of DPN of rats.}, } @article {pmid40669445, year = {2025}, author = {Omary, L and Canfora, EE and Puhlmann, ML and Gavriilidou, A and Rijnaarts, I and Holst, JJ and Op den Kamp-Bruls, YMH and de Vos, WM and Blaak, EE}, title = {Intrinsic chicory root fibers modulate colonic microbial butyrate-producing pathways and improve insulin sensitivity in individuals with obesity.}, journal = {Cell reports. Medicine}, volume = {6}, number = {7}, pages = {102237}, pmid = {40669445}, issn = {2666-3791}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Butyrates/metabolism ; *Cichorium intybus/chemistry ; *Colon/microbiology/metabolism ; Diabetes Mellitus, Type 2 ; *Dietary Fiber ; *Gastrointestinal Microbiome/drug effects ; *Insulin Resistance ; *Obesity/microbiology/metabolism/diet therapy ; Plant Roots/chemistry/metabolism ; Triglycerides/blood ; }, abstract = {Type 2 diabetes and obesity have become major public health concerns. Growing evidence suggests that increased dietary fiber intake, through its interaction with the gut microbiota, may help prevent these diseases. Here, we demonstrate in a 12-week randomized, placebo-controlled trial in individuals at risk for type 2 diabetes that intake of an intrinsic fiber product, consisting of entire plant cells, tended to improve peripheral insulin sensitivity (p = 0.085), increased whole-body insulin sensitivity (p = 0.032), reduced circulating triglycerides (p = 0.049), and tended to reduce intrahepatic lipid content (p = 0.063), along with an increased proportion of small adipocytes (p = 0.008). Phylogenetic and metagenomic analysis revealed that these outcomes coincided with increased levels of fiber-degrading Bifidobacterium spp. and butyrate-producing Anaerostipes spp. and a functional shift toward a distal butyrogenic trophic chain while the best responding individuals had increased levels of pectin degraders that may produce propionate. Our findings demonstrate the pivotal role of slowly fermented, intrinsic plant cell fibers in improving cardiometabolic health. This study was registered at ClinicalTrials.gov (NCT04714944).}, } @article {pmid40669246, year = {2025}, author = {Liu, S and Chen, Q and Dong, C and Qiu, X and Li, W and Tang, K}, title = {Impact of coastal deoxygenation on antibiotic resistance gene profiles in size-fractionated bacterial communities.}, journal = {Marine pollution bulletin}, volume = {220}, number = {}, pages = {118445}, doi = {10.1016/j.marpolbul.2025.118445}, pmid = {40669246}, issn = {1879-3363}, abstract = {Oxygen loss disrupts marine ecosystems, threatening biodiversity and causing mass mortality of marine life. Antibiotic resistance genes (ARGs) pose a significant threat to human health by promoting the spread of resistant pathogens, making infections harder to treat and increasing mortality risks. However, the interplay between deoxygenation and ARG dynamics remains poorly understood. In this study, we employed time-series metagenomics to investigate the responses of ARG profiles in free-living (FL) and particle-associated (PA) fraction to oxygen loss during a 22-day summer deoxygenation event in the East China Sea. In total, we identified 1,186 ARG subtypes and 2,279 mobile genetic element (MGE) subtypes. The most dominant resistance classes of antibiotics were multidrug (23.5%), followed by tetracycline (15%), macrolide-lincosamide-streptogramin (13.4%), peptide (10.3%), glycopeptide (8.7%), aminoglycoside (7.3%), and beta-lactam (4.9%). We found that ARG richness in FL fraction increased with declining oxygen levels, particularly for beta-lactam and multidrug class, while no significant relationship was observed in the PA fraction. Although the total relative abundance of ARGs in both fraction showed no significant oxygen dependence, beta-lactam and multidrug resistance genes in FL fraction significantly increased with oxygen loss. Co-occurrence network analysis revealed stronger positive associations between ARGs and MGEs in the FL fraction, suggesting enhanced gene transfer among environmental bacteria. Furthermore, neutral community model analysis indicated that stochastic processes also played an interactive role in shaping ARG composition dynamics in both bacterial fractions. Our findings provide evidence that coastal deoxygenation preferentially enriches high-risk ARGs (e.g., beta-lactamase genes) in FL bacteria through MGE-mediated transfer, highlighting escalating antibiotic resistance risks that threaten both ecosystem and human health under climate warming. This study offers a framework for size-fractionated ARG monitoring and targeted mitigation strategies in coastal ecosystems.}, } @article {pmid40668000, year = {2025}, author = {Jiang, D and Hurst, JH and Mohamed, G and Kelly, MS and Roper, J and Surana, NK}, title = {Decreased Microbiota-Driven Tyrosine Metabolism Is Associated With Symptomatic COVID-19 in Children.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf325}, pmid = {40668000}, issn = {1537-6613}, abstract = {BACKGROUND: The gut microbiota has been implicated in driving coronavirus disease 2019 (COVID-19) disease severity, but the underlying mechanisms remain unknown. We investigated the relationship between the gut microbiota and development of symptomatic COVID-19 in children.

METHODS: We prospectively collected stool and plasma samples from 229 children who were exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including 45 COVID-19 negative, 57 with asymptomatic COVID-19, and 127 with symptomatic COVID-19. We performed shotgun metagenomic sequencing on the stool samples to characterize the microbial taxa and functional profiles. Plasma cytokine levels were measured in SARS-CoV-2-infected individuals.

RESULTS: Children with symptomatic COVID-19 had reduced microbial biodiversity and decreased functional capacity for several metabolic pathways, including a reduction in the tyrosine biosynthesis pathway, as compared to SARS-CoV-2-uninfected children or those with asymptomatic infection. The abundance of the tyrosine biosynthesis pathway was associated with plasma levels of interferon alpha (IFN-α), which were lower in children with symptomatic COVID-19.

CONCLUSIONS: Our findings highlight a relationship between the ability of the gut microbiota to metabolize tyrosine and the development of COVID-19 symptoms in children. More generally, our study suggests that the gut microbiota may help protect against more severe forms of COVID-19, potentially by modulating IFN-α.}, } @article {pmid40667647, year = {2025}, author = {Yan, C and Li, XN and Peng, ZL and Wu, W and Wang, Z and Zhu, ZR and Liu, JC and Wang, Y and Ren, JL and Zhang, ZY and Li, JT}, title = {Hologenomics Reveals Specialized Dietary Adaptations in the Mengla Snail-Eating Snake.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e09999}, doi = {10.1002/advs.202509999}, pmid = {40667647}, issn = {2198-3844}, support = {2024NSFSC1181//Sichuan Science and Technology Program/ ; 2024YFHZ0294//Sichuan Science and Technology Program/ ; 32325011//National Natural Science Foundation of China/ ; 32220103004//National Natural Science Foundation of China/ ; 32370449//National Natural Science Foundation of China/ ; 32300351//National Natural Science Foundation of China/ ; }, abstract = {Serpents, as highly adaptable vertebrates, provide robust models for studying the mechanisms of dietary specialization. Using an integrative multi-omics approach, encompassing host genomic, transcriptomic, proteomic, gut metagenomic, and enzymatic analyses, the mechanisms underlying dietary adaptations in the Mengla snail-eating snake (Pareas menglaensis), a species specialized in consuming snails is investigated. Adaptations supporting this diet included evolution of infralabial glands secreting toxin homologs and digestive enzymes, facilitating molluscan predation and digestion. This specialization has driven adaptive evolution in the host genome and shaped the gut microbiota, addressing both nutritional challenges (e.g., lipid deficiency) and digestive requirements (e.g., mucus degradation) associated with snail consumption. Notably, the functional convergence in microbial gene functions between reptiles and mammals highlights parallel evolutionary pathways in dietary specialization. These findings elucidate the genomic foundations of dietary specialization in P. menglaensis, offering broader insights into evolutionary adaptation within a holobiome framework.}, } @article {pmid40667420, year = {2025}, author = {Orejudo, M and Gómez, MJ and Riestra, S and Rivero, M and Gutiérrez, A and Rodríguez-Lago, I and Fernández-Salazar, L and Ceballos, D and Benítez, JM and Aguas, M and Bastón-Rey, I and Bermejo, F and Casanova, MJ and Lorente-Poyatos, RH and Ber, Y and Ginard, D and Esteve, M and de Francisco, R and García, MJ and Francés, R and Rodríguez, A and Alcaide Suárez, N and Guerra Del Río, E and Soto, P and Nos, P and Barreiro-de Acosta, M and Guerra, I and Hervías Cruz, D and Domínguez Cajal, M and Royo, V and Aceituno, M and Aldars-García, L and Garre, A and Ramírez, C and Soleto, I and Schuppe-Koistinen, I and Engstrand, L and Baldán-Martín, M and Sánchez-Cabo, F and Gisbert, JP and Chaparro, M}, title = {Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1595884}, pmid = {40667420}, issn = {2235-2988}, mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Crohn Disease/microbiology ; Colitis, Ulcerative/microbiology ; Young Adult ; Aged ; Computational Biology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; }, abstract = {INTRODUCTION: Dysbiosis is a key mechanism in inflammatory bowel disease (IBD) pathophysiology. Previous microbiota studies in IBD generally have involved patients treated with immunosuppressive agents, which can affect the results. We aimed to elucidate the fecal microbiota composition in newly diagnosed treatment-naïve IBD patients.

METHODS: Microbiota from stool samples were investigated using shotgun metagenomics sequencing and subsequent bioinformatics analysis.

RESULTS: A total of 103 patients with Crohn's disease (CD), 144 with ulcerative colitis (UC), and 49 healthy controls (HC) were included. CD patients had significantly lower species-level diversity than those with UC and HC. CD subgroups with Ileocolonic location and stricturing behavior showed reduced diversity compared to HC. A negative correlation was observed between endoscopic severity and microbial diversity in CD patients. UC patients had similar microbial diversity to HC, which was unaffected by disease activity. Taxonomic abundance analysis revealed a tendency towards a higher relative abundance of Escherichia coli and a lower relative abundance of Faecalibacterium prausnitzii in IBD patients compared to HC. However, the most significant differences in these patients compared to HC were observed in less abundant species, such as Toxoplasma gondii, Gemella morbillorum, and several species of the Adlercreutzia genera. Functional analysis in these patients highlighted changes in carbohydrate and nucleotide pathways.

DISCUSSION: Our data suggest that newly diagnosed CD patients show significant microbiota composition disparities compared to UC patients and HC. Microbiota differences in these patients are linked to dysbiosis, characterized by a reduction in beneficial genera such as Gemella and Adlercreutzia, and a rise in pathogenic species.}, } @article {pmid40665424, year = {2025}, author = {Yvenou, S and Le Moigne, M and Rouxel, O and Aubé, J and Trouche, B and Cathalot, C and Rinnert, E and Philippon, X and Chéron, S and Boissier, A and Guyader, V and Germain, Y and Godfroy, A and Roussel, EG and Alain, K}, title = {Sulfur-rich deposits associated with the deep submarine volcano Fani Maoré support broad microbial sulfur cycling communities.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {166}, pmid = {40665424}, issn = {2049-2618}, support = {ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; Sino-French IRP 1211 MicrobSea//CNRS-INEE/ ; Sino-French IRP 1211 MicrobSea//CNRS-INEE/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; }, mesh = {*Sulfur/metabolism/analysis ; *Volcanic Eruptions/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; *Geologic Sediments/microbiology/chemistry ; Indian Ocean ; Metagenomics/methods ; Seawater/microbiology/chemistry ; Metagenome ; }, abstract = {BACKGROUND: In 2018, the island of Mayotte located in the western Indian ocean, has experienced a seismo-volcanic crisis linked to the birth of an impressive intraplate submarine volcano at the east of the island. This volcano, named Fani Maoré, which has not yet been the subject of microbiological studies, triggered the largest submarine eruptive event ever recorded. Close to the volcano's summit is a singular meter-size structure containing abundant native sulfur mineralizations. While a wide variety of ecosystems, with more or less well documented microbial communities, are found in active volcanoes on the ocean floor, knowledge on microbial communities hosted in habitats such as sulfur-rich intraplate volcanoes, that are not located on hotspots, remains limited. Genome-resolved metagenomics, culture-based functional approaches, geochemical and mineralogical analyses were combined to characterize the geological and physico-chemical constraints of the environment surrounding the yellow deposit part of this hotspot volcano and the composition and functions of its microbial community.

RESULTS: Geological and geochemical analyses indicated that this volcanic habitat had high concentrations in various sulfur species, including native sulfur, hydrogen sulfide and sulfate. Twenty-three Metagenome Assembled Genomes (MAGs) belonging to 8 different bacterial phyla, mainly Pseudomonadota, Bacteroidota and Campylobacterota, were reconstructed from the sulfur-rich deposit and analyzed. The vast majority of MAGs encoded genes for complete sulfur cycling metabolic pathways, in particular sulfur oxidation. Estimation of the cultivable microbial fraction revealed a diversity of microorganisms, with high growth rates for sulfur reduction, sulfate reduction with dihydrogen, and sulfur oxidation. Sulfur compound (S[0], SO3[2-] and S2O3[2-]) disproportionation was also observed in cultures. The versatile genus Sulfurimonas was prevalent in culture at 6 and 20 °C, in the presence of different sulfur redox couples.

CONCLUSIONS: Microbial communities, including taxa commonly found in ridge hydrothermal systems, were composed of autotrophic, heterotrophic or mixotrophic taxa using a large range of electron donors and acceptors to fuel their catabolism, particularly sulfur compounds in all common oxidation states. They had the genetic potential and physiological capacity to carry out all the metabolic reactions of the microbial sulfur cycle using the abiotic sulfur compounds present in their habitat. Representatives of the Sulfurimonas genus were among the main chemoautotrophs, since they predominated in eleven different temperature-redox pair culture combinations. Based on the observations, a conceptual model was proposed to describe the interactions in this sulfur-rich deposit that may occur between the microorganisms, the physico-chemical conditions and the sulfur compounds supplied by the environment. Video Abstract.}, } @article {pmid40665409, year = {2025}, author = {Lyu, L and Fan, Y and Vogt, JK and Clos-Garcia, M and Bonnefond, A and Pedersen, HK and Dutta, A and Koivula, R and Sharma, S and Allin, KH and Brorsson, C and Cederberg, H and Chabanova, E and De Masi, F and Dermitzakis, E and Elders, PJ and Blom, MT and Hollander, M and Eriksen, R and Forgie, I and Frost, G and Giordano, GN and Grallert, H and Haid, M and Hansen, TH and Jablonka, B and Kokkola, T and Mahajan, A and Mari, A and McDonald, TJ and Musholt, PB and Pavo, I and Prehn, C and Ridderstråle, M and Ruetten, H and Hart, LM' and Schwenk, JM and Stankevic, E and Thomsen, HS and Vangipurapu, J and Vestergaard, H and Viñuela, A and Walker, M and Hansen, T and Linneberg, A and Nielsen, HB and Brunak, S and McCarthy, MI and Froguel, P and Adamski, J and Franks, PW and Laakso, M and Beulens, JWJ and Pearson, E and Pedersen, O}, title = {The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {78}, pmid = {40665409}, issn = {1756-994X}, support = {FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics ; Blood Glucose ; Europe ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; Metagenomics ; *Prediabetic State/microbiology/metabolism ; Prospective Studies ; }, abstract = {BACKGROUND: Previous case-control studies have reported aberrations of the gut microbiota in individuals with prediabetes. The primary objective of the present study was to explore the dynamics of the gut microbiota of individuals with prediabetes over 4 years with a secondary aim of relating microbiota dynamics to temporal changes of metabolic phenotypes.

METHODS: The study included 486 European patients with prediabetes. Gut microbiota profiling was conducted using shotgun metagenomic sequencing and the same bioinformatics pipelines at study baseline and after 4 years. The same phenotyping protocols and core laboratory analyses were applied at the two timepoints. Phenotyping included anthropometrics and measurement of fasting plasma glucose and insulin levels, mean plasma glucose and insulin under an oral glucose tolerance test (OGTT), 2-h plasma glucose after an OGTT, oral glucose insulin sensitivity index, Matsuda insulin sensitivity index, body mass index, waist circumference, and systolic and diastolic blood pressure. Measures of the dynamics of bacterial microbiota were related to concomitant changes in markers of host metabolism.

RESULTS: Over 4 years, significant declines in richness were observed in gut bacterial and viral species and microbial pathways accompanied by significant changes in the relative abundance and the genetic composition of multiple bacterial species. Additionally, bacterial-viral interactions diminished over time. Despite the overall reduction in bacterial richness and microbial pathway richness, 80 dominant core bacterial species and 78 core microbial pathways were identified at both timepoints in 99% of the individuals, representing a resilient component of the gut microbiota. Over the same period, individuals with prediabetes exhibited a significant increase in glycemia and insulinemia alongside a significant decline in insulin sensitivity. Estimates of the gut bacterial microbiota dynamics were significantly correlated with temporal impairments in host metabolic health.

CONCLUSIONS: In this 4-year prospective study of European patients with prediabetes, the gut microbiota exhibited major changes in taxonomic composition, bacterial species genetics, and microbial functional potentials, many of which paralleled an aggravation of host metabolism. Whether the temporal gut microbiota changes represent an adaptation to the progression of metabolic abnormalities or actively contribute to these in prediabetes cases remains unsettled.

TRIAL REGISTRATION: The Diabetes Research on Patient Stratification (DIRECT) study, an exploratory observational study initiated on October 15, 2012, was registered on ClinicalTrials.gov under the number NCT03814915.}, } @article {pmid40665020, year = {2025}, author = {Liu, Y and Zhang, H and Cao, L and Fu, L and Lian, C and Guo, Y and Zhong, Z and Seim, I and Wang, M and Li, C}, title = {Methane filtration and metabolic cooperation of microbial communities in cold seep water columns from South China Sea.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1052}, pmid = {40665020}, issn = {2399-3642}, support = {42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; China ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Metagenome ; *Water Microbiology ; Oceans and Seas ; Metagenomics ; }, abstract = {Microbes in cold seep water columns are essential for methane sequestration and biogeochemical cycling, yet their structures and ecological functions, particularly at the bottom water interface (BWI), are poorly understood. Here, we performed metagenomic analyses to explore the microbial biodiversity and functions at the F-site cold seep in the South China Sea. Functional stratification revealed that photosynthetic autotrophs dominate surface zones, heterotrophs are prevalent in mesopelagic zones, and chemosynthetic bacteria are abundant at the BWI. We obtained 377 metagenome-assembled-genomes (MAGs) and constructed genome-scale metabolic models to unveil metabolic interactions facilitating the coupling of carbon, nitrogen, and sulfur among microbes, particularly at the BWI. Notably, methanotrophic bacteria with diverse metabolic capabilities distributed from the BWI zone to the deep mesopelagic regions, highlighting the broader influence of methane. In conclusion, our findings reveal a high degree of heterogeneity in the composition and function of microorganisms across the F-site cold seep water column. Our study also sheds light on the ecological interactions and environmental gradients that shape these microbial communities.}, } @article {pmid40664945, year = {2025}, author = {Jiang, W and Xi, R and Zhou, J and Pei, Y and Huang, P and Liu, M}, title = {16S rRNA and Metagenomic Datasets of Gastrointestinal Microbiota in Fetal and 7-Day-Old Goat Kids.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1234}, pmid = {40664945}, issn = {2052-4463}, mesh = {Animals ; *Goats/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Metagenome ; Fetus/microbiology ; }, abstract = {The perinatal period (from late gestation to the neonatal stage) in ruminants is a critical phase for fetal organ maturation, where ecological succession of gastrointestinal microbial communities significantly impacts livestock production efficiency. However, research remains insufficient regarding the distribution patterns and functional annotation of microbial communities across different gastrointestinal compartments during this period. This study characterized early microbiota dynamics in Hutianshi Goats using 16S rRNA sequencing (4 fetal goats at 90 ± 10 gestational days) and metagenomics (3 7-day-old goat kids). The fetal goat group generated 852,694 valid reads, yielding 688,277 high-quality reads after chimera removal for downstream analysis. The 7-day-old goat kids group produced 1,081,588,182 final valid reads, after data processing and assembly, 8,561,345 contigs were generated. Gene prediction identified 6,095,352 genes. Multi-database annotations (NR, KEGG, CAZy, etc.) revealed functional potential and antimicrobial resistance traits. The public release of this dataset facilitates academic understanding of microbial community dynamics and host-microbe interactions during this developmental stage, providing both theoretical foundations and data resources for ruminant developmental biology and precision breeding regulation.}, } @article {pmid40663936, year = {2025}, author = {Wang, Z and Rong, XL and Dai, CX and Wang, Q and Lu, LF and Zhang, WT and Zhang, L and Chen, QQ and Liu, EH}, title = {Fucoidan alleviates renal fibrosis in mice via Akkermansia muciniphila-mediated suppression of NEU1-TLR4-NFκB signaling axis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {157060}, doi = {10.1016/j.phymed.2025.157060}, pmid = {40663936}, issn = {1618-095X}, mesh = {Animals ; *Polysaccharides/pharmacology ; NF-kappa B/metabolism ; Toll-Like Receptor 4/metabolism ; Fibrosis/drug therapy ; Mice ; Signal Transduction/drug effects ; Male ; Kidney/pathology/drug effects ; Neuraminidase/metabolism ; Gastrointestinal Microbiome/drug effects ; Humans ; *Kidney Diseases/drug therapy ; Mice, Inbred C57BL ; Disease Models, Animal ; Akkermansia ; Ureteral Obstruction ; Cell Line ; Epithelial-Mesenchymal Transition/drug effects ; }, abstract = {BACKGROUND: Fucoidan, a bioactive sulfated polysaccharide, is renowned for its extensive range of biological activities, including anticancer activity, antioxidative properties, immune activation and has demonstrated supportive therapeutic effects in treating kidney ailments. However, the underlying mechanism related to renal fibrosis remains not fully understood.

PURPOSE: The aim of this study was to elucidate the protective effects and mechanism of FPS against renal fibrosis with a focus on gut-kidney axis.

METHODS: We established renal fibrosis models in mice using unilateral ureteral obstruction (UUO), folic acid (FA) challenge, or a microbiota-depleted, with continuous oral administration of FPS, Akkermansia muciniphila (AKK), or acetate at specified doses and intervals. Simultaneously, we examined the impact of FPS on epithelial mesenchymal transformation in cultured HK-2 and investigated the associated mechanisms.

RESULTS: In this study, we demonstrate that fucoidan administration reduces renal collagen deposition, inflammation, epithelial mesenchymal transformation and improves renal function in mouse models of renal fibrosis induced by UUO or FA. Metagenomics analysis showed that fucoidan significantly increases the abundance of AKK by promoting its growth in UUO-induced renal fibrosis. Oral administration of live AKK alleviates renal fibrosis in UUO and FA mouse models. Using oral antibiotic-treated mice, we found that the effect of fucoidan on renal fibrosis was weakened. Gas chromatography-mass spectrometry (GC-MS/MS) study results show that AKK produces the short-chain fatty acids (acetate), which protects against renal fibrosis by suppressing NEU1-TLR4-NFκB-mediated inflammation in the kidney.

CONCLUSION: Our findings establish a novel gut-kidney axis wherein fucoidan ameliorates renal fibrosis through AKK-mediated acetate production and subsequent NEU1-TLR4-NFκB pathway inhibition.}, } @article {pmid40661966, year = {2025}, author = {Yao, C and Xue, X and Jia, Y and Li, M and Zhang, L and Yuan, H and Xue, H and Hu, R}, title = {Rosuvastatin ameliorates obesity-associated insulin resistance in high-fat diet-fed mice by modulating the gut microbiota and gut metabolites.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1593581}, pmid = {40661966}, issn = {2235-2988}, mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; *Obesity/drug therapy/complications/metabolism ; *Rosuvastatin Calcium/pharmacology/administration & dosage ; Mice, Inbred C57BL ; Male ; Mice ; Fatty Acids, Volatile/metabolism/analysis ; Disease Models, Animal ; Feces/microbiology/chemistry ; Metabolomics ; Metagenomics ; Bacteria/classification/genetics/drug effects ; }, abstract = {INTRODUCTION: Insulin resistance (IR) underlies metabolic diseases such as obesity and diabetes. Statins are lipid-lowering drugs that have also been studied to improve insulin resistance, but the mechanism is not well understood. Metagenomics and metabolomics were used to analyze the main species and metabolic pathways involved in intestinal microbes while improving insulin resistance in mice with rosuvastatin in this study.

METHODS: C57BL/6J male mice fed a high-fat diet were used to establish the insulin resistance (IR) mouse model. Rosuvastatin (RSV) was then administered for 8 weeks. Metagenomics and metabolomics were utilized to analyze the microbial composition and short chain fatty acid metabolites in intestinal feces of mice.

RESULTS: It was observed that insulin-resistant mice showed significant improvement in insulin resistance following treatment with RSV. In comparison to the HFD group, specific bacterial strains were significantly increased, and the levels of butyric acid, caproic acid, and isovaleric acid among the short-chain fatty acids were notably elevated in the RSV group. Through KEGG enrichment analysis, 19 dominant strains and 15 key enzymes involved in butyric acid metabolism were identified.

CONCLUSIONS: The results suggested that IR mice might enhance insulin sensitivity by promoting butyric acid synthesis via intestinal microbes following RSV treatment.}, } @article {pmid40661950, year = {2025}, author = {Ma, Y and Suo, J and Sheng, S and Chen, L}, title = {PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1622744}, pmid = {40661950}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *B7-H1 Antigen/genetics/deficiency ; Mice ; Mice, Knockout ; *Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism ; Dysbiosis ; Disease Models, Animal ; Severity of Illness Index ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic autoimmune disorder driven by gut microbiota dysbiosis. As an essential immune checkpoint, Programmed death-ligand 1 (PD-L1) has been implicated in modulating gut microbiota composition. However, the precise role of PD-L1 in shaping metagenomic profiles during IBD-associated colitis remains unexplored.

METHODS: DSS-induced colitis was established in both PD-L1 knockout (Pdcd1lg1-/-) mice and wild-type (wt) control mice. Clinical parameters, including disease activity index (DAI), body weight changes, colon length, and histopathological alterations, were systematically evaluated using non-parametric Kruskal-Wallis tests and ANOVA to compare colitis severity between genotypes.

RESULTS: PD-L1 knockout mice exhibited exacerbated colitis, manifesting significantly greater weight loss (p<0.05 vs. wt_DSS), colonic shortening (p<0.05), and DAI scores (p<0.05) and inflammatory changes. PD-L1 knockout mice showed distinct dysbiosis, with enriched pathobionts (Escherichia coli, p=0.006; Bacteroides thetaiotaomicron, p=0.015) and depletion of commensals (Tritrichomonas foetus, p<0.001; Ligilactobacillus murinus). Alpha diversity analysis using Chao1 index revealed statistically significant differences between experimental groups (p=0.05). The transporters downregulate anti-inflammatory SCFA metabolism. KEGG enrichment analysis of differentially expressed genes (DEGs) revealed significant associations with immune and inflammatory pathways in PD-L1 knockout mice.

CONCLUSION: PD-L1 deficiency aggravates colitis by driving pathogenic microbiota alterations and impairing microbial metabolic homeostasis, highlighting its dual regulatory roles in immune homeostasis and microbiome dynamics.}, } @article {pmid40660333, year = {2025}, author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Gao, Y and Zhang, Y and Li, X and Ai, B and Wei, S and Tian, F and Jia, G and Lin, H and Chen, Z and Zhang, Z}, title = {Exposure to ambient air pollution over developmental stages induced neurodevelopmental impairment in mice offspring via microbiome-gut-brain axis.}, journal = {Particle and fibre toxicology}, volume = {22}, number = {1}, pages = {20}, pmid = {40660333}, issn = {1743-8977}, support = {2024A1515010465//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022A1515010695//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82203988//National Natural Science Foundation of China/ ; 2023A04J2071//Guangzhou Municipal Science and Technology Project/ ; 23qnpy107//Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Air Pollution/adverse effects ; Mice ; Male ; *Neurodevelopmental Disorders/chemically induced/microbiology ; Pregnancy ; *Prenatal Exposure Delayed Effects/chemically induced ; *Brain/drug effects/growth & development ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; *Brain-Gut Axis/drug effects ; }, abstract = {Exposure to air pollution has been increasingly recognized as a risk factor for neurodevelopmental disorders, and gut microbiome may play a critical role. However, current evidence still remains scarce. In the present study, mice were exposed to real-time ambient air pollution from conception through young adulthood, with neurobehavioral performance and gut microbiome being assessed across different developmental stages. Neurodevelopmental changes including emotional and cognitive impairments were observed in behavioral tests, accompanied by pathological and inflammation changes in brain, which were more pronounced in adolescence than in young adulthood. Alterations in the compositions and functions of gut microbiome were also revealed by fecal metagenomic sequencing. Mediation analysis showed that gut microbiome alterations significantly contributed to the observed neurodevelopmental changes induced by air pollution. Furthermore, after antibiotic (ABX) intervention, the observed neurobehavioral, pathological and inflammatory differences between the exposed and control groups diminished. These findings indicate that the gut microbiome mediates the neurodevelopmental damage caused by exposure to air pollution during developmental stages, adding novel insights on the underlying mechanisms linking air pollution and neurodevelopmental disorders.}, } @article {pmid40659687, year = {2025}, author = {Zhang, N and Zhao, Y and Zhang, Z and Zhan, M and Zhao, X and Zhang, Y and Sun, J and Zhang, Y and Teng, L and Liu, Z}, title = {Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1219}, pmid = {40659687}, issn = {2052-4463}, support = {32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Transcriptome ; Metagenomics ; *Ranidae/genetics/microbiology ; *Metagenome ; Climate Change ; Microbiota ; China ; Adaptation, Physiological ; }, abstract = {Global climate change has become a primary driving factor behind the biodiversity crisis in amphibians, making it crucial to understand how climate change affects species and their potential responses. The plateau brown frog (Rana kukunoris) is often regarded as an ideal ecological indicator species, yet research on its environmental adaptation mechanisms based on transcriptomic and microbiomic studies remains limited. Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). We gathered transcriptomic data from three tissues (blood, liver, and muscle), resulting in 294,962 unigenes and 570,192 transcripts. Metagenomic sequencing identified major bacterial groups, including Firmicutes, Proteobacteria, Bacteroidetes, Spirochetes, and Actinobacteria. In summary, the results of this study can be used to further explore the associations among microbiota, host, and environment, which are crucial for comprehending the mechanisms of environmental adaptation in this species and contributing to the conservation of amphibian biodiversity.}, } @article {pmid40659674, year = {2025}, author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J}, title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1222}, pmid = {40659674}, issn = {2052-4463}, support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; }, abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.}, } @article {pmid40658106, year = {2025}, author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F}, title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.}, journal = {Environmental science & technology}, volume = {59}, number = {29}, pages = {15203-15214}, doi = {10.1021/acs.est.5c06047}, pmid = {40658106}, issn = {1520-5851}, mesh = {*Arsenic ; *Soil/chemistry ; Methylation ; Soil Microbiology ; Microbiota ; Oryza ; }, abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.}, } @article {pmid40657968, year = {2025}, author = {Morandi, SC and Uldry, AC and Eldridge, N and Kreuzer, M and Herzog, EL and Zinkernagel, M and Zysset-Burri, DC}, title = {Toward the Characterization of the Human Core Ocular Surface Microbiome.}, journal = {Investigative ophthalmology & visual science}, volume = {66}, number = {9}, pages = {40}, pmid = {40657968}, issn = {1552-5783}, mesh = {Humans ; *Microbiota/genetics ; Middle Aged ; Adult ; *Tears/microbiology/metabolism ; *Conjunctiva/microbiology ; Female ; Male ; Tandem Mass Spectrometry ; *Eyelids/microbiology ; *Bacteria/genetics/isolation & purification ; Chromatography, Liquid ; Eye Proteins/metabolism ; }, abstract = {PURPOSE: The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.

METHODS: Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60 years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.

RESULTS: At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.

CONCLUSIONS: The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.}, } @article {pmid40657495, year = {2025}, author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F}, title = {Correction: Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1644681}, doi = {10.3389/fmicb.2025.1644681}, pmid = {40657495}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1515939.].}, } @article {pmid40656756, year = {2025}, author = {Huang, Y}, title = {Investigation of protists in Momoge wetland (China) through metagenomic next-generation sequencing.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e153721}, pmid = {40656756}, issn = {1314-2828}, abstract = {The Momoge wetland plays an important role in maintaining the ecosphere and protist is an indispensable component of it. In order to reveal community structure and diversity of protists in Momoge wetland, metagenomic next-generation sequencing (mNGS) was performed. The main results are as follows: 1) A total of 224 species were identified, belonging to 17 phyla, 32 classes, 75 orders, 94 families and 146 genera. Among them, Bacillariophyta, Evosea, Oomycota, Rhodophyta, Ciliophora, Haptophyta, and Salpingoecarosetta, Guillardiatheta, Polarellaglacialis, Cladocopiumgoreaui were the dominant phyla and species, respectively; 2) Most of them were species adapted to the saline-alkali environment, and the protists of Momoge wetland had higher diversity, fewer dominant species, and higher evenness than those of the harsher environment; 3) KEGG analysis showed that some protistan pathways were related to the saline-alkali environmental adaptation. This research is beneficial to ecological protection and provides valuable information for future studies.}, } @article {pmid40653476, year = {2025}, author = {Bi, BY and Lin, L and Huang, L and Zhou, J and Yan, WJ and Huang, L and Wang, J and Li, XB}, title = {Effects of arabinoxylan on BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex and intestinal microbiome in post-stroke depressed rats.}, journal = {BMC neuroscience}, volume = {26}, number = {1}, pages = {40}, pmid = {40653476}, issn = {1471-2202}, support = {No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; }, mesh = {Animals ; *Prefrontal Cortex/metabolism/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Signal Transduction/drug effects ; Rats ; Receptor, trkB/metabolism ; *Depression/metabolism/drug therapy/etiology ; *Xylans/pharmacology ; Rats, Sprague-Dawley ; *Stroke/complications/metabolism ; Cyclic AMP Response Element-Binding Protein/metabolism ; }, abstract = {AIM: To explore the effects of arabinoxylan on the BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex of post-stroke depressed rats, and to explore its neuronal protective effects through the microbial-gut-brain axis in the regulation of this pathway.

METHODS: The rat model of post-stroke depression (PSD) was established by middle cerebral artery occlusion (MCAO) combined with chronic unpredictable mild stimulation (CUMS). They were randomly divided into 5 groups (blank control, post-stroke depression, arabinoxylan, fluoxetine hydrochloride, fluoxetine hydrochloride combined arabinoxylan). The rats were treated differently for 28 days according to their grouping. Body mass, sugar and water consumption experiments and open-field experiments were used to evaluate the behavior of rats. The pathological changes were observed by H&E staining. The expression levels of amine neurotransmitters were detected by ELISA. The expression levels of BDNF mRNA and BDNF, TrkB and p-CREB were detected by RT-PCR and Western blot. The analysis of intestinal metagenomics was conducted by 16 S rDNA sequencing.

RESULTS: Compared with the post-stroke depression group, the body weight, activity and sugar water consumption rate of the arabinoxylan group were increased. The expression levels of 5-HT in the prefrontal cortex, colon and serum levels of 5-HT, DA and NE were increased. The expression levels of BDNF mRNA and BDNF, TrkB and P-CREB in the prefrontal cortex were also upregulated. The number of neurons in the prefrontal cortex increased; Colon mucosal injury and inflammatory cell infiltration decreased, the intestinal microbial diversity increased; The relative abundance of probiotics such as bifidobacterium, Christensenia, Dubosiella New York and ruminococcus increased. The relative abundance of Prevotella NK3B31 group was reduced. The level of 5-HT in the prefrontal cortex was negatively correlated with the abundance of Prevotellaceae NK3B31 group.

CONCLUSION: Arabinoxylan improved depressive-like behavior in rats and its neuroprotective role was achieved by promoting the growth of intestinal probiotics, improving the intestinal barrier, affecting the BDNF/TrkB/p-CREB signaling pathway, and increasing the expression levels of monoamine neurotransmitters 5-HT, DA and NE.}, } @article {pmid40652256, year = {2025}, author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J}, title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {162}, pmid = {40652256}, issn = {2049-2618}, mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.

RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.

CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.}, } @article {pmid40650758, year = {2025}, author = {Kearns, R}, title = {Gut modulation to regulate NF-κB in colorectal and gastric cancer therapy and inflammation.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {8}, pages = {264}, pmid = {40650758}, issn = {1432-0851}, mesh = {Humans ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/immunology ; *Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; *Inflammation/metabolism ; *Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; Animals ; Dysbiosis ; Fecal Microbiota Transplantation ; Signal Transduction ; }, abstract = {The nuclear factor-kappa B (NF-κB) pathway plays a pivotal role in cancer progression, immune regulation, and inflammation. Aberrant activation of this pathway, often driven by gut microbiota dysbiosis, contributes to tumorigenesis, therapy resistance, and chronic inflammation. Emerging evidence highlights the bidirectional interaction between gut microbiota and NF-κB signalling, suggesting that microbiota modulation may enhance cancer treatment efficacy and reduce treatment-induced inflammation. This review explores the mechanistic underpinnings of gut microbiota-mediated NF-κB regulation, focusing on microbial metabolites such as short-chain fatty acids (SCFAs) and microbial-associated molecular patterns, including lipopolysaccharides (LPS). It examines how conventional cancer treatments, chemotherapy, radiotherapy, and immune checkpoint inhibitors, exacerbate dysbiosis and NF-κB-driven inflammation, further complicating treatment outcomes. Additionally, this review evaluates the therapeutic potential of gut-targeted interventions, including probiotics, prebiotics, faecal microbiota transplantation (FMT), and dietary modifications, in restoring microbial homeostasis and modulating NF-κB signalling. Despite promising findings, challenges remain regarding the clinical translation of microbiota-based therapies, including the need for standardised microbiota profiling, regulatory frameworks, and long-term safety assessments. Advances in metagenomics and metabolomics are proposed as essential tools to personalise gut-targeted interventions and optimise cancer treatment strategies. Integrating gut modulation into oncology represents a paradigm shift, offering a holistic, patient-centric approach to cancer therapy. However, further research is required to validate these strategies and ensure their efficacy in clinical applications.}, } @article {pmid40650567, year = {2025}, author = {Wallenius, AJ and Venetz, J and Zygadlowska, OM and Lenstra, WK and van Helmond, NAGM and Dalcin Martins, P and Slomp, CP and Jetten, MSM}, title = {A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {8}, pages = {}, pmid = {40650567}, issn = {1574-6941}, support = {NWO VI.Veni.222.332/NWO_/Dutch Research Council/Netherlands ; VI.Veni.212.040/NWO_/Dutch Research Council/Netherlands ; OCENW.XS22.3.043/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/genetics/classification ; Eutrophication ; Phylogeny ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification ; Lakes/microbiology ; Netherlands ; *Microbiota ; Sulfates/metabolism ; Metagenomics ; }, abstract = {Coastal areas contribute over 75% of global marine methane emissions, a proportion predicted to increase with anthropogenic eutrophication and deoxygenation. Prolonged low oxygen and high organic matter input can disrupt the methane cycle, favoring methane production over oxidation. However, factors influencing this imbalance remain unclear. Here, we show that methanogenesis dominates microbial methane cycling in the anoxic sediments of eutrophic coastal marine Lake Grevelingen (The Netherlands) after summer stratification. A shallow sulfate-methane transition zone (SMTZ; 5-15 cm depth) was observed, with high methane concentrations below. Methane was produced in all investigated layers, while methane oxidation was restricted to the narrow SMTZ. Amplicon sequencing, metagenomics, and incubations revealed a metabolically and phylogenetically diverse methanogenic community with niche separation, and methylotrophic methanogenesis prevalent in all layers. Two clades of ANME archaea, ANME-2a/b and ANME-3, were restricted to a narrow zone together with their putative syntrophic sulfate-reducing bacteria, coinciding with the observed methane oxidation activity. Our results suggest that eutrophication and deoxygenation will further contribute to rising methane emissions, tilting the microbial methane cycle toward increased methanogenesis, and decreasing the efficiency of the microbial methane filter.}, } @article {pmid40650408, year = {2025}, author = {Beau, A and Natividad, J and Benoit, B and Delerive, P and Duboux, S and Feng, Y and Jammes, M and Barnel, C and Sequino, G and Pinteur, C and Glorieux, G and Fouque, D and Vidal, H and Koppe, L}, title = {A specifically designed multi-biotic reduces uremic toxin generation and improves kidney function.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2531202}, pmid = {40650408}, issn = {1949-0984}, mesh = {Humans ; *Uremic Toxins/metabolism ; *Renal Insufficiency, Chronic/microbiology/therapy ; Animals ; *Probiotics/administration & dosage ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Cresols/metabolism ; *Kidney/physiology ; Prebiotics/administration & dosage ; Female ; Middle Aged ; Lactobacillus/metabolism/growth & development ; *Uremia ; Cellobiose/metabolism ; Rats ; Indican ; Bacteria/metabolism/genetics/classification ; Disease Models, Animal ; }, abstract = {Chronic kidney disease (CKD) is characterized by accumulation of uremic toxins (UTs), such as p-cresyl sulfate and indoxyl sulfate, generated through the transformation of tyrosine and tryptophan by the gut microbiota. Using an ex vivo Simulator of the Human Intestinal Microbial Ecosystem (SHIME) colonized with fecal samples from eight CKD patients or nine healthy volunteers, a higher bacterial generation of p-cresol and indoles post-amino acid enrichment, as well lower basal butyrate levels, in the feces of CKD patients were found. Through in silico data mining, we selected a probiotic strain lacking the capacity to produce UT, i.e. without genes for tryptophanase, tyrosinase and urease. In vitro, we confirmed the potential of cellobiose as a prebiotic supporting the growth of this strain. We further designed a novel specific multi-biotic for CKD (SynCKD) [containing a probiotic Lactobacillus johnsonii NCC533, a prebiotic (1% cellobiose), and a postbiotic (1% short and medium chain triglycerides C4-C8, a source of butyrate)]. SynCKD effectively curtailed UT precursor generation ex vivo. The in vivo efficacy of SynCKD (and the synergic effect) was established in two uremic rodent models, demonstrating lower plasma levels of UTs and enhancing kidney function after 6-8 weeks of treatment. These effects were linked to better gut microbial ecology. Metagenomic analysis revealed reduced microbial genes for tryptophan/tyrosine degradation. This study lays the foundation for SynCKD as a potential therapy to mitigate CKD progression.}, } @article {pmid40649719, year = {2025}, author = {Popov, IV and Manakhov, AD and Gorobets, VE and Diakova, KB and Lukbanova, EA and Malinovkin, AV and Venema, K and Ermakov, AM and Popov, IV}, title = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.}, journal = {International journal of molecular sciences}, volume = {26}, number = {13}, pages = {}, pmid = {40649719}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Animals ; *Chiroptera/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Phylogeny ; *Metagenome ; }, abstract = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.}, } @article {pmid40647338, year = {2025}, author = {Decembrino, N and Scuderi, MG and Betta, PM and Leonardi, R and Bartolone, A and Marsiglia, R and Marangelo, C and Pane, S and De Rose, DU and Salvatori, G and Grosso, G and Di Domenico, FM and Dotta, A and Putignani, L and Capolupo, I and Di Benedetto, V}, title = {Microbiota-Modulating Strategies in Neonates Undergoing Surgery for Congenital Gastrointestinal Conditions: A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {13}, pages = {}, pmid = {40647338}, issn = {2072-6643}, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; Probiotics/administration & dosage/therapeutic use ; Dysbiosis/microbiology/prevention & control ; Prebiotics/administration & dosage ; *Gastrointestinal Diseases/surgery/microbiology/congenital ; Anti-Bacterial Agents/therapeutic use ; Milk, Human ; *Digestive System Surgical Procedures ; Enteral Nutrition ; }, abstract = {Background/Objectives: The gut microbiota (GM) is pivotal for immune regulation, metabolism, and neurodevelopment. Infants undergoing surgery for congenital gastrointestinal anomalies are especially prone to microbial imbalances, with a paucity of beneficial bacteria (e.g., Bifidobacteria and Bacteroides) and diminished short-chain fatty acid production. Dysbiosis has been associated with severe complications, including necrotizing enterocolitis, sepsis, and feeding intolerance. This narrative review aims to critically examine strategies for microbiota modulation in this high-risk cohort. Methods: An extensive literature analysis was performed to compare the evolution of GM in healthy neonates versus those requiring gastrointestinal surgery, synthetizing strategies to maintain eubiosis, such as early nutritional interventions-particularly the use of human milk-along with antibiotic management and supplementary treatments including probiotics, prebiotics, postbiotics, and lactoferrin. Emerging techniques in metagenomic and metabolomic analysis were also evaluated for their potential to elucidate microbial dynamics in these patients. Results: Neonates undergoing gastrointestinal surgery exhibit significant alterations in microbial communities, characterized by reduced levels of eubiotic bacteria and an overrepresentation of opportunistic pathogens. Early initiation of enteral feeding with human milk and careful antibiotic stewardship are linked to improved microbial balance. Adjunctive therapies, such as the administration of probiotics and lactoferrin, show potential in enhancing gut barrier function and immune modulation, although confirmation through larger-scale studies remains necessary. Conclusions: Modulating the GM emerges as a promising strategy to ameliorate outcome in neonates with congenital gastrointestinal surgical conditions. Future research should focus on the development of standardized therapeutic protocols and the execution of rigorous multicenter trials to validate the efficacy and safety of these interventions.}, } @article {pmid40646273, year = {2025}, author = {Mikolas, M and Fauszt, P and Petrilla, A and Nemeth, P and David, P and Szilagyi-Tolnai, E and Szilagyi-Racz, A and Stagel, A and Gal, F and Gal, K and Sohajda, R and Szoke, Z and Hossain, SA and Stundl, L and Biro, S and Remenyik, J and Paholcsek, M}, title = {Analysis of ICU resistome dynamics in patients, staff and environment for the identification of predictive biomarkers of sepsis and early mortality.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {25080}, pmid = {40646273}, issn = {2045-2322}, mesh = {Humans ; *Intensive Care Units ; *Sepsis/mortality/microbiology ; Biomarkers/analysis ; Male ; Female ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Aged ; *Drug Resistance, Multiple, Bacterial ; Health Personnel ; Oropharynx/microbiology ; Bacteria/drug effects/genetics ; Microbiota ; Drug Resistance, Bacterial ; }, abstract = {Antimicrobial resistance (AMR) is a global crisis, posing a critical challenge to healthcare systems, particularly in intensive care units (ICUs), where multidrug-resistant organisms (MDROs) threaten patient survival. This study offers a unique, real-world perspective on AMR dynamics by analyzing 96 metagenomic samples from three key sources: oropharyngeal and rectal swabs of deceased ICU patients (both postadmission and antemortem), healthcare workers, and high-touch ICU surfaces. Findings revealed the ICU environment as a major AMR reservoir, with oropharyngeal swabs carrying the highest AMR burden. While healthcare staff facilitated MDRO spread, they were not primary sources. Staff microbiomes' MDRO pattern closely resembled environmental samples. Key AMR species included B. fragilis, E. coli, S. pneumoniae, S. aureus, with P. aeruginosa persisting on high-touch surfaces. Tetracycline resistance was the most prevalent, with common resistances comprising 36.1% of all detected AMR markers. Staff microbial community exhibited higher resistance to macrolides, fluoroquinolones, lincosamides, and cephamycins. A 10-day survival threshold distinguished early (EM) and late mortality (LM) groups. EM patients exhibited unique AMR species in the oropharynx, suggesting respiratory-driven infections, while LM patients showed greater gut-associated resistance. Higher rectal AMR counts correlated with prolonged survival. Notably, four key MDROs (L. monocytogenes, M. tuberculosis, S. haemolyticus, and S. agalactiae) were enriched in sepsis patients, suggesting early risk markers. Fewer new resistances emerged in rectal than oropharyngeal swabs, likely due to antibiotic selection pressure. Vancomycin and levofloxacin, frequently co-administered, exerted stronger selective pressure in the oropharynx, possibly explaining the high MRSA prevalence in patient and environmental samples.}, } @article {pmid40645966, year = {2025}, author = {Kim, S and Park, MS and Kang, I and Cho, JC}, title = {Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1201}, pmid = {40645966}, issn = {2052-4463}, support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NRF-2022R1C1C2004070//National Research Foundation of Korea (NRF)/ ; }, mesh = {Republic of Korea ; *Lakes/microbiology ; *Metagenome ; *Microbiota ; Metagenomics ; Ecosystem ; Fresh Water/microbiology ; }, abstract = {Lake ecosystems play a fundamental role in the global biogeochemical cycling of essential elements such as carbon, nitrogen, and phosphorus. Microorganisms within these ecosystems mediate key processes that regulate these cycles. Metagenomic analyses provide valuable insights into the taxonomic and functional diversity of microbial communities in various environments, including freshwater habitats. Here, we present a comprehensive metagenomic dataset derived from Lake Soyang, the largest freshwater reservoir in South Korea. A total of 28 metagenomes were generated from water samples collected across two distinct sampling periods: the first set (n = 8) was obtained between April 2014 and January 2015 from two depths (1 m and 50 m) in four different seasons, while the second set (n = 20) was collected between January 2019 and November 2019 from five depths (1, 10, 20, 40, and 90 m) over four seasons. Metagenomic sequencing yielded 9.3-21.8 Gbp per sample. This dataset provides a valuable resource for future studies exploring the ecophysiological characteristics of microbial communities in pelagic freshwater environments.}, } @article {pmid40645948, year = {2025}, author = {Calayag, AM and Priest, T and Oldenburg, E and Muschiol, J and Popa, O and Wietz, M and Needham, DM}, title = {Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6427}, pmid = {40645948}, issn = {2041-1723}, mesh = {Arctic Regions ; Seasons ; *Seawater/virology/microbiology ; Metagenome ; *Virome/genetics ; Oceans and Seas ; *DNA Viruses/genetics/classification/isolation & purification ; Biodiversity ; Bacteria/virology/genetics ; Host Microbial Interactions ; }, abstract = {Viruses of microbes play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemistry. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. Here, we study dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5662 vOTUs, 98% and 2% are Caudoviricetes and Megaviricetes, respectively. Viral coverage is, on average, 5-fold higher than cellular coverage, and 8-fold higher in summer. Viral community composition shows annual peaks in similarity and strongly correlates with prokaryotic community composition. Using network analysis, we identify putative virus-host interactions and six ecological modules associated with distinct environmental conditions. The network reveals putative novel cyanophages with time-lagged correlations to their hosts (in late summer) as well as diverse viruses correlated with Flavobacteriaceae, Pelagibacteraceae, and Nitrosopumilaceae. Via global metagenomes, we find that 42% of Fram Strait vOTUs peak in abundance in high latitude regions of both hemispheres, and encode proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding viral regulation and ecosystem impacts in changing polar oceans.}, } @article {pmid40645041, year = {2025}, author = {Pei, J and Chen, S and Yu, K and Liang, J and Zhang, R and Li, P and Hou, Z and Fu, L and Ma, H}, title = {Microbial regulation of dissolved organic matter revealed by integrated metabolomics and metagenomics in the World's deepest blue hole.}, journal = {Marine environmental research}, volume = {210}, number = {}, pages = {107354}, doi = {10.1016/j.marenvres.2025.107354}, pmid = {40645041}, issn = {1879-0291}, mesh = {Metagenomics ; Metabolomics ; *Microbiota ; Nitrogen/analysis ; Seawater/microbiology/chemistry ; China ; *Environmental Monitoring ; Sulfur/analysis ; *Water Microbiology ; }, abstract = {Dissolved organic matter (DOM) is central to marine biogeochemical cycles, with its composition and dynamics closely linked to microbial communities. In oxygen-stratified extreme environments, however, the ecological relationships between DOM and microbes remain insufficiently explored. This study explores the dynamics of DOM and microbial communities in the Sansha Yongle Blue Hole, the world's deepest ocean blue hole, using an integrated metabolomics and metagenomics approach. Our findings elucidate significant alterations in microbial communities and DOM composition in response to variations in oxygen concentrations. Specifically, various DOM components, including dissolved organic sulfur (DOS) and dissolved organic nitrogen (DON), along with a spectrum of small molecule metabolites, were affected by microbial metabolic activities. Higher concentrations of DOS in the anoxic layer were positively correlated with increased sulfur metabolism in microbial communities, whereas lower concentrations of DON in the chemocline were associated with the coupling of nitrification and denitrification processes. Additionally, metabolites such as lipids, amino acids, isovalerylcarnitine, and peptides, associated with microbial physiological functions, energy metabolism, and signal transduction processes, varied with oxygen stratification. These findings contribute to a deeper understanding of the intricate relationships between microbial communities and DOM dynamics in extreme marine environments.}, } @article {pmid40642988, year = {2025}, author = {Wang, F and Wu, Y and Ni, J and Xie, Q and Shen, J and Chen, H and Ma, C and Yao, Y and Wang, J and Xu, L and Xiang, Q and Zhao, Y and Chen, Y and Li, L}, title = {Gut microbiota links to histological damage in chronic HBV infection patients and aggravates fibrosis via fecal microbiota transplantation in mice.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0076425}, pmid = {40642988}, issn = {2165-0497}, mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; *Gastrointestinal Microbiome/physiology ; Mice ; Humans ; *Liver Cirrhosis/pathology/microbiology ; *Hepatitis B, Chronic/microbiology/pathology/complications ; *Dysbiosis/microbiology ; Feces/microbiology ; Male ; Liver/pathology ; Bacteria/classification/genetics/isolation & purification ; Bile Acids and Salts/metabolism ; Female ; Middle Aged ; Disease Models, Animal ; Mice, Inbred C57BL ; Hepatitis B virus ; }, abstract = {Gut microbiota dysbiosis has been observed in HBV-related cirrhosis, but its role in early-stage disease and its correlation with liver pathology remain unclear. Moreover, whether dysbiosis is a cause or consequence of liver cirrhosis is still debated. We recruited 20 treatment-naïve patients with chronic HBV infection, assessing liver injury via biopsy. Fecal metagenomic sequencing was used to analyze the correlation between gut microbiota and liver histology. To explore the causality, fecal samples from an HBV-related cirrhosis patient were transplanted into mice with CCl4-induced liver fibrosis. Patients with significant histological damage exhibited reduced alpha diversity and greater microbial homogeneity. Species such as Eubacterium_sp_CAG_180, Gemmiger_formicilis, and Oscillibacter_sp_ER4 had decreased abundance, while Parabacteroides_distasonis, Bacteroides_dorei, and Bacteroides_finegoldii were enriched. Mice receiving fecal transplants from the cirrhotic patient showed aggravated liver fibrosis, with increased collagen deposition; elevated ALT, AST, and ALP levels; and heightened hepatic inflammatory gene expression. Additionally, abnormal bile acid profiles with elevated unconjugated bile acids (e.g., GCA and CA) were observed. Gut microbiota dysbiosis is closely associated with liver histological damage in chronic HBV infection and may drive fibrosis progression via microbial-bile acid interactions. These findings suggest potential for gut microbiota-based assessment and treatment strategies in chronic hepatitis B.IMPORTANCEThis study elucidates a significant association between gut microbiota dysbiosis and liver histological damage in patients with chronic hepatitis B (HBV), potentially exacerbating fibrosis progression through bile acid interactions. By analyzing patient gut microbiota and conducting fecal transplant experiments in mice, researchers have identified that gut microbiota dysbiosis contributes to hepatic fibrosis during chronic HBV infection. These findings underscore the importance of the gut-liver axis in HBV disease progression, indicating that monitoring or modulating gut bacteria may facilitate early diagnosis or therapeutic interventions. This research bridges the gap in understanding whether microbial alterations drive disease progression or result from it, providing a foundation for developing therapies targeting the microbiome to mitigate liver damage in chronic HBV infections.}, } @article {pmid40640914, year = {2025}, author = {Zhao, J and Kui, L and Huang, J and Deng, J and Liu, L and Zhu, C and Shi, Y and Li, C and Xiao, Y and Yu, J and Li, Q and Yang, B and Leng, B and Chan, H}, title = {Bifidobacterium animalis subsp. Lactis BX-BC08 modulates gut microbiota and secretes alpha-Ketoglutaric acid to alleviate MC903-induced atopic dermatitis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {768}, pmid = {40640914}, issn = {1479-5876}, support = {SL2024A04J01394//Guangzhou Municipal Science and Technology Bureau Young Doctor "Qihang" Program/ ; }, mesh = {Animals ; *Dermatitis, Atopic/microbiology/chemically induced/drug therapy ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis/physiology/metabolism ; *Ketoglutaric Acids/metabolism ; Mice ; Disease Models, Animal ; Female ; Probiotics ; Mice, Inbred BALB C ; }, abstract = {OBJECTIVE: Bifidobacterium is known to be depleted in patients with atopic dermatitis (AD). This study aims to investigate the potential prophylactic effects of Bifidobacterium animalis subsp. lactis BX-BC08 (B. lactis BX-BC08) in a murine model of AD.

DESIGN: The immunosuppressive and anti-inflammatory effects of BX-BC08 were evaluated in a MC903-induced AD mouse model. Gut microbiota composition was analyzed by metagenomic sequencing, while high-performance liquid chromatography-mass spectrometry (HPLC-MS) was employed to identify anti-inflammatory molecules produced by B. lactis BX-BC08.

RESULTS: BX-BC08 significantly attenuated pro-inflammatory responses, scaling and swelling in the MC903-induced AD like murine model compared to controls. Fecal microbial profiling revealed an enrichment of probiotics and a reduction of pro-inflammatory bacteria in BX-BC08 treated mice. Metabolic analysis of BX-BC08 bacteria culture supernatant and treated mice identified a significant enrichment of alpha-Ketoglutaric acid (AKG). Functional validation in the murine AD model demonstrated that AKG strongly suppressed T helper 2 (Th2)-driven pro-inflammatory responses.

CONCLUSION: BX-BC08 mitigates AD-like inflammation by producing the anti-inflammatory metabolite AKG. BX-BC08 could serve as a novel prophylactic agent for AD prevention.}, } @article {pmid40640502, year = {2025}, author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T}, title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24821}, pmid = {40640502}, issn = {2045-2322}, support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; }, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; }, abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.}, } @article {pmid40640272, year = {2025}, author = {Xie, Y and Xiang, JY and Long, L and Ma, Y and Xing, Z and Wang, L and Shao, C and Liu, N and Li, F}, title = {Impact of different treatment methods and timings on soil microbial communities with transgenic maize straw return.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24820}, pmid = {40640272}, issn = {2045-2322}, support = {20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; 20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; }, mesh = {*Zea mays/genetics ; *Soil Microbiology ; *Plants, Genetically Modified ; *Microbiota ; Soil/chemistry ; Agriculture/methods ; Crops, Agricultural ; Metagenomics/methods ; }, abstract = {Understanding the impact of genetically modified (GM) crop straw return on soil ecosystems is crucial as GM crops become more prevalent. This study assesses the effects of straw mulching and deep tillage on soil microbial communities from GM and non-GM maize, highlighting potential ecological impacts. Shotgun metagenomic sequencing was utilized to analyze the microbial community structure and functional genes in soil samples collected at different times (30, 180, and 270 days) after straw mulching and deep tillage treatments. The study included insect-resistant transgenic maize varieties 2A-7 and CM8101 and their non-transgenic counterparts B73 and Zheng58. Different treatment methods significantly affect soil microbial alpha-diversity and beta-diversity, with deep tillage resulting in higher alpha-diversity compared to mulching, and the 180-day mark exhibiting the highest alpha-diversity across all sampling times. Early straw treatment prompted a rapid microbial response to nutrient availability, with notable changes in diversity and function over time. Straw treatments notably altered soil microbial functions, especially in carbon cycling and nutrient metabolism. Interestingly, the microbial effects of GM versus non-GM maize straw were similar, suggesting crop residue type under consistent soil management practices might not significantly alter microbial community structures. The methods and timing of straw treatments have a significant impact on soil microbial communities, surpassing the differences between GM and non-GM straw. These findings highlight the importance of straw management practices for sustainable agricultural ecosystem management.}, } @article {pmid40639969, year = {2025}, author = {Shi, C and Wang, C and He, J and Zhang, M and Huang, W}, title = {Epichloë Endophytes Potentially Facilitate Host Plant Recruitment of Rhizosphere Microbiota Carrying Beneficial Traits.}, journal = {Physiologia plantarum}, volume = {177}, number = {4}, pages = {e70397}, doi = {10.1111/ppl.70397}, pmid = {40639969}, issn = {1399-3054}, support = {31760704//National Natural Science Foundation of China/ ; 2022D01A79//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 23XJTRZW07//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; }, mesh = {*Rhizosphere ; *Endophytes/physiology ; Plant Roots/microbiology ; *Epichloe/physiology ; *Microbiota/physiology ; Soil Microbiology ; Symbiosis ; }, abstract = {Plant-microbe symbiotic relationships drive ecosystem evolution. This study employed metabolomics and metagenomic technologies to investigate the effects of the aboveground-restricted endophytic fungus Epichloë guerinii in the host plant Melica transsilvanica on the rhizosphere microbial community structure and functional traits. Our results revealed that the presence of E. guerinii significantly increased the secretion of organic acids, amino acids, and sugar alcohols from the host root system. These exudates correlated strongly with abundant, plant growth-promoting rhizosphere microorganisms like Pseudomonas, Bradyrhizobium, and Nitrospira. Functional genes that were significantly enriched in the host rhizosphere microbiota were predominantly associated with biofilm formation and organic acid metabolic pathways. Co-enrichment analyses of rhizosphere soil metabolites and genes highlighted pathways such as flagellar assembly and carbon/nitrogen/sulfur metabolism. Notably, the abundance of key genes governing the flagellar motor MotA protein in the host rhizosphere, as well as those involved in the reductive tricarboxylic acid (rTCA) cycle, nitrification, and thiosulfate oxidation, were significantly elevated. This study demonstrates that E. guerinii positively regulates rhizosphere microbial community functions by reprogramming the composition of host root exudates. These findings deepen the mechanistic understanding of Epichloë-plant-rhizosphere microbe interactions.}, } @article {pmid40639330, year = {2025}, author = {Liu, K and Wang, Y}, title = {Metatranscriptomics catches gut microbes in the act.}, journal = {Cell host & microbe}, volume = {33}, number = {7}, pages = {1040-1042}, doi = {10.1016/j.chom.2025.06.004}, pmid = {40639330}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Humans ; *Transcriptome ; *Bacteria/genetics ; *Metagenome ; Animals ; Circadian Rhythm ; *Gastrointestinal Tract/microbiology ; }, abstract = {In this issue of Cell Host & Microbe, Flores Ramos et al.[1] employ metatranscriptomics to uncover diurnal microbial functional shifts in the gut microbiome driven by time-restricted feeding. Their work highlights the value of metatranscriptomics over metagenomics in capturing real-time microbial activity and guiding therapeutic bacterial engineering.}, } @article {pmid40638549, year = {2025}, author = {Dasgupta, S}, title = {Unraveling the Microbiome-Asthma Axis: Metagenomic Insights from Airway and Gut Microbial Communities.}, journal = {Omics : a journal of integrative biology}, volume = {29}, number = {8}, pages = {374-383}, doi = {10.1177/15578100251358958}, pmid = {40638549}, issn = {1557-8100}, mesh = {Humans ; *Asthma/microbiology ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; Dysbiosis/microbiology ; *Microbiota ; *Respiratory System/microbiology ; }, abstract = {Asthma is a heterogeneous respiratory disease with complex pathogenesis involving immune dysregulation, environmental triggers, and increasingly recognized to have contributions from the human microbiome. Emerging evidence from longitudinal birth cohorts and multi-omics studies reveals that early-life microbial colonization patterns in both the gastrointestinal and respiratory tracts play a crucial role in shaping immune trajectories and influencing asthma susceptibility. This expert review highlights the findings from pivotal studies that associate dysbiosis in the gut and airway microbiota with asthma development and its diverse phenotypic manifestations. Reduced abundance of immunomodulatory genera such as Bifidobacterium, Faecalibacterium, and Lachnospira in the gut has been consistently associated with increased asthma risk. In the airways, increased colonization by potentially pathogenic taxa, including Moraxella, Haemophilus, and Streptococcus, correlates with viral respiratory infections and persistent wheezing. Microbiome diversity patterns also differ between asthma phenotypes: eosinophilic asthma typically features a community profile closer to healthy individuals, while neutrophilic asthma is marked by enrichment of pro-inflammatory bacterial species. Moreover, protective genera such as Dolosigranulum and Corynebacterium in the upper airways are associated with lower risk of asthma and reduced respiratory infections. Elucidating these microbiome-mediated mechanisms holds promise for the development of targeted microbiota-based strategies for asthma prevention and phenotype-specific therapeutic interventions. The present review unpacks these localized microbial patterns and their mechanistic implications for asthma development, severity, and endotypic variation. Finally, unraveling the microbiome-asthma axis from airway and gut microbial communities also has implications for new ways of thinking personalized medicine in the future.}, } @article {pmid40637407, year = {2025}, author = {Chin, HS and Ravi Varadharajulu, N and Teo, KC and Cheong, PCH and Tang, S-L}, title = {Key findings from 15 years of Mangrovibacter research: a generalist bacterium beyond endophytes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0247924}, doi = {10.1128/aem.02479-24}, pmid = {40637407}, issn = {1098-5336}, abstract = {Since the discovery of Mangrovibacter plantisponsor in 2010, research on Mangrovibacters (MGBs) has stagnated. Although laboratories worldwide have isolated various MGB strains and deposited their 16S rDNA sequences in the NCBI database, a limited understanding of MGBs has resulted in only a few publications from these collections. Recent advancements in metagenomic technology have revealed the presence of MGBs in a broader range of habitats. Most microbiomes exhibit low MGB abundance (typically <1%). Even in environments with higher prevalence, such as salt-tolerant aerobic granular sludge (75%), the gut of superworms fed with polyurethane (22%), or fermented foods like mandai (16%), the functional roles of MGBs remain unclear. Through meticulous curation of publications and data from MicrobeAtlas and AMIBASE, MGBs can be classified as free living, endophytic, or zoonotic. Recent evidence suggests their presence in food sources and potential interactions with humans. Current studies confirm the coexistence of MGBs with humans. This review underscores the phenotypic features and genomic foundations of MGBs, highlighting attributes such as endophytic behavior, diverse metabolite utilization, tolerance to salinity and pH, metal homeostasis, biofilm formation, and bioremediation potential. Insights are derived from the analysis of four MGB genomes deposited in NCBI since 2014, along with three newly reported genomes in 2024. Experimental and genetic evidence suggests that MGBs act as "generalist microbes" capable of thriving in diverse nutrient sources and harsh environments. This review elucidates prospective research trajectories and highlights numerous potential commercial applications of MGBs, emphasizing the need for further investigation into their roles and benefits.}, } @article {pmid40636496, year = {2025}, author = {Ding, Z and Xu, Y and Wang, Y and Liu, M and Zhu, P and Cui, K and Yang, C and Xu, C and Feng, T and Liu, Q}, title = {Host-driven remodeling of rumen microbiota supports lactation metabolism in buffalo.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1617388}, pmid = {40636496}, issn = {1664-302X}, abstract = {INTRODUCTION: Rumen microbiota and host metabolites play a key role in regulating ruminant production performance and physiological adaptation. However, the interplay between host physiological status and rumen microbial-metabolite dynamics across lactation stages in buffaloes remains unclear.

METHODS: This study employed a multi-omics approach, integrating metagenomic and serum metabolomic analyses, to investigate microbial remodeling and metabolic adaptations in buffaloes during lactation and dry periods.

RESULTS: Metagenomic analysis revealed increased abundances of Anaerovibrio, Succiniclasticum, and Methanobrevibacter_A during lactation, associated with lipid hydrolysis, propionate production, and methanogenesis, respectively. Glycoside hydrolase families GH2, GH3, GH5, and GH13 were enriched, indicating elevated carbohydrate degradation potential. In contrast, Butyrivibrio, Fibrobacter, and Eubacterium_Q were predominant during the dry period, contributing to fiber degradation and butyrate synthesis. Functional pathways related to niacin metabolism, bicarbonate reabsorption, and neuroactive ligand-receptor interaction were significantly upregulated during lactation. Metabolomic profiling identified lactation-enriched metabolites such as indole-3-methylacetate, D-maltose, and gluconic acid, correlating with immune and metabolic indicators (e.g., IgA, glucose, LDL). Conversely, dry period metabolites such as 1-methylhistidine and 5-hydroxyindoleacetic acid indicated physiological shifts toward tissue repair and stress mitigation.

DISCUSSION: The integrative analysis revealed that host physiological demands during lactation coordinate rumen microbial restructuring to enhance triglyceride degradation, fatty acid biosynthesis, and energy mobilization, thereby supporting milk production. These findings provide novel insights into the host-driven microbiome-metabolite axis underlying lactation in buffaloes.}, } @article {pmid40635073, year = {2025}, author = {Zhao, GH and Zhou, BB and Cao, ZH and Xiao, T and Li, YN and Zhu, WJ and Sun, H and Xie, HH and Xie, XM and Zhang, JM and Wang, Q and Zhang, X and Xie, JJ and Dong, HJ and Xu, C and Yin, K}, title = {The development and excretion of Toxoplasma gondii oocyst manipulate the gut microbiota in its definitive host.}, journal = {Parasites & vectors}, volume = {18}, number = {1}, pages = {273}, pmid = {40635073}, issn = {1756-3305}, support = {202401050157//The Health Science and Technology Development Program of Shandong Province/ ; 202401050156//The Health Science and Technology Development Program of Shandong Province/ ; 202201050466//The Health Science and Technology Development Program of Shandong Province/ ; ZR2023QH253//The Natural Science Foundation of Shandong Province/ ; ZR2022MH197//The Natural Science Foundation of Shandong Province/ ; tsqn202103186//The Taishan Scholars Project of Shandong Province/ ; 202407//Joint Innovation Team for Clinical & Basic Research/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Toxoplasma/growth & development/physiology ; Cats ; *Oocysts/growth & development/physiology ; *Toxoplasmosis, Animal/parasitology/microbiology ; Bacteria/genetics/classification ; Metagenomics ; Feces/parasitology ; Host-Parasite Interactions ; }, abstract = {BACKGROUND: Oocysts serve as the primary source of Toxoplasma infection. Therefore, understanding oocyst development and exploring effective strategies to prevent oocyst excretion are crucial for controlling toxoplasmosis.

METHODS: In this study, shotgun metagenomics was employed to characterize the functional and compositional changes in the gut microbiota of cats during oocyst development. The Spearman correlation test was utilized to analyze the correlation between differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZymes) in key bacteria regulating oocyst excretion.

RESULTS: The results revealed that group A (sexual initiation stage) displayed a lower number of functional genes, which were restored to normal levels in group B (oocyst excretion stage), compared with group C (Toxoplasma-uninfected samples). The abundance of 39 KEGG pathways, 106 CAZymes, and 98 virulence factors (VFs) varied significantly among the three groups. The atrazine degradation pathway, associated with sexual development, was upregulated in group B. CAZymes involved in restoring the intestinal mucosal barrier and VFs related to iron metabolism, antibiotic resistance, and suppression of host immunity were enriched in group B. Sexual initiation and oocyst excretion resulted in reduced gut bacterial diversity and microbiota dysbiosis. Probiotics and bacteria related to linoleic acid (LA) uptake were dominant in both group A and group B. Bacteroides stercoris was the most significantly upregulated bacterium and could influence the expression of carbohydrate-binding modules (CBMs) and glycoside hydrolases (GHs) in group B.

CONCLUSIONS: During the oocyst development/excretion stage, the function and composition of the cat gut microbiota changed significantly. In addition, Bacteroides stercoris may play a crucial role in oocyst excretion by regulating key candidates of CBMs and GHs. Our findings lay the foundation for investigating the regulatory mechanisms of oocyst excretion.}, } @article {pmid40634275, year = {2025}, author = {Özçam, M and Lin, DL and Gupta, CL and Li, A and Gomez, JC and Wheatley, LM and Baloh, CH and Sanda, S and Jones, SM and Lynch, SV}, title = {Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6330}, pmid = {40634275}, issn = {2041-1723}, support = {AI148104//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UM1 AI109565/AI/NIAID NIH HHS/United States ; T32 DK007762/DK/NIDDK NIH HHS/United States ; UM1AI160040//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UM1 AI160040/AI/NIAID NIH HHS/United States ; P01 AI089473/AI/NIAID NIH HHS/United States ; AI128482//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI089473//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01 AI148104/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/immunology/physiology ; *Bile Acids and Salts/metabolism ; *Peanut Hypersensitivity/therapy/immunology/microbiology ; Feces/microbiology/chemistry ; *Arachis/immunology ; *Amino Acids/metabolism ; Male ; Administration, Oral ; Female ; Child ; *Desensitization, Immunologic/methods ; Double-Blind Method ; Child, Preschool ; Treatment Failure ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Antigens, Plant/immunology ; }, abstract = {Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome has been linked to food allergy, we sought to identify fecal predictors of POIT efficacy and mechanistic insights into treatment response. Here, we conducted a secondary analysis of the IMPACT randomized, double-blind, placebo-controlled POIT trial (NCT01867671), using longitudinal fecal samples from 90 children, and performed 16S rRNA sequencing, shotgun metagenomics, and untargeted metabolomics. Integrated multi-omics analyses revealed a relationship between gut microbiome metabolic capacity and treatment outcomes. Five fecal bile acids present prior to treatment initiation predicted POIT efficacy (AUC 0.71). Treatment failure was associated with a specific bile acid profile, enhanced amino acid utilization, and higher copy number of the ptpA gene encoding a bacterial hydrolase that cleaves tripeptides containing proline residues - a feature of immunogenic peanut Ara h 2 proteins. In vitro, peanut-supplemented fecal cultures of children for whom POIT failed to induce remission evidenced reduced Ara h 2 concentrations. Thus, distal gut microbiome metabolism appears to contribute to POIT failure.}, } @article {pmid40631381, year = {2025}, author = {Huang, X and Gao, X and Fan, Y and Wang, D and Chen, X and Qi, X and Yang, Z and Wang, YE and Meng, J and Zou, G and Liu, Z and Li, X}, title = {Moderate altitude exposure impacts extensive host-microbiota multi-kingdom connectivity with serum metabolome and fasting blood glucose.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2530660}, pmid = {40631381}, issn = {2150-5608}, mesh = {Humans ; *Altitude ; *Metabolome ; *Gastrointestinal Microbiome ; Male ; Female ; *Blood Glucose/analysis ; Adult ; Feces/microbiology ; Mycobiome ; Bacteriophages ; Fasting/blood ; Young Adult ; Bacteria/classification/genetics ; Metagenomics ; *Host Microbial Interactions ; China ; Middle Aged ; Archaea ; Fatty Acids, Volatile ; }, abstract = {The contributions and interactions of multi-kingdom microbiota (i.e. bacteriome, mycobiome, archaeome, and phageome) with serum metabolome and host phenome in healthy individuals under moderate altitude exposure remain unclear. We applied shotgun metagenomic sequencing in feces and targeted metabolomics technology in serum to explore how human gut multi-kingdom microorganisms influence the serum metabolome and phenome in healthy Chinese individuals following moderate altitude exposure. The results indicated that individuals with moderate altitude exposure exhibited more substantial alterations in gut bacteriome and phageome compared to those in mycobiome and archaeome. Both intra-kingdom and inter-kingdom correlations at baseline were denser than those following moderate altitude exposure. Bacteriophages-host interaction analysis revealed symbiosis between bacteriophages and Bacteroidetes, Proteobacteria, and short-chain fatty acids (SCFAs) producers. Furthermore, bacteriophage Shirahamavirus PTm1 (odds ratio (OR) = 3.82; 95% confidence interval (CI): 1.20-12.16), archaeon Crenarchaeota (OR = 3.70; 95% CI: 1.35-10.14) and bacterium Bacteroidetes (OR = 3.69; 95% CI: 1.34-10.15) showed a positive association with lowered fasting blood glucose (FBG) benefits, while bacteriophage Candidatus Nitrosopelagicus brevis (OR = 0.30; 95% CI: 0.10-0.89) and butyric acid (OR = 0.07; 95% CI: 0.01-0.37) exhibited a negative association with lowered FBG benefits. These findings suggest that targeting gut multi-kingdom microorganisms could serve as an alternative therapeutic approach to mitigate dysglycemia and its associated metabolic disorders.}, } @article {pmid40630933, year = {2025}, author = {Takács, B and Jaksa, G and Qorri, E and Gyuris, Z and Pintér, L and Haracska, L}, title = {Advancing metagenomic classification with NABAS+: a novel alignment-based approach.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {3}, pages = {lqaf092}, pmid = {40630933}, issn = {2631-9268}, mesh = {Humans ; *Metagenomics/methods ; Algorithms ; *Software ; *Sequence Alignment/methods ; *Metagenome ; Microbiota/genetics ; }, abstract = {Microbiome research has expanded rapidly in the last decade due to advances in sequencing technology, resulting in larger and more complex data. This has also led to the development of a plethora of metagenomic classifiers applying different algorithmic principles to classify microorganisms. However, accurate metagenomic classification remains challenging due to false positives and the need for dataset-specific tuning, limiting the comparability of distinct studies and clinical use. In this study, we demonstrate the discrepancy between current, commonly used classifiers and propose a novel classifier, NABAS+ (Novel Alignment-based Biome Analyzing Software+). NABAS+ uses BWA (Burrows-Wheeler aligner) alignment with strict RefSeq curation to ensure one reliable genome per species and filters for genomes with only high-quality reads for precise species-level identification from Illumina shotgun data. The performance of our algorithm and three commonly used classifiers was evaluated on in silico datasets modelling human gastrooral communities, as well as on deeply sequenced microbial community standards. Additionally, we illustrated the usefulness of NABAS+ in detecting pathogens in real-world clinical data. Our results show that NABAS+, due to its extensive alignment process, is superior in accuracy and sensitivity compared to leading microbiome classifiers, particularly in reducing false positives in deep-sequenced microbial samples, making it suitable for clinical diagnosis.}, } @article {pmid40628728, year = {2025}, author = {Arp, G and Jiang, AK and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, MR and Li, Y and Hall, B and Jiang, X}, title = {Identification of gut bacteria reductases that biotransform steroid hormones.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6285}, pmid = {40628728}, issn = {2041-1723}, support = {R35 GM155208/GM/NIGMS NIH HHS/United States ; T32 AI089621/AI/NIAID NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology/genetics ; Humans ; Phylogeny ; Male ; Female ; *Oxidoreductases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification ; *Steroids/metabolism ; Biotransformation ; Pregnenolone/metabolism ; *Bacterial Proteins/metabolism/genetics ; }, abstract = {The metabolism of steroid hormones by the gut microbiome is increasingly recognized as a key factor in human health; however, the specific enzymes mediating these transformations remain largely unidentified. In this study, we identify Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, we show that 5β-reductase evolved to specialize in converting both natural and synthetic 3-ketosteroid hormones into their 5β-reduced derivatives, while Δ[6]-3-ketosteroid reductase adapted to produce Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the conversion of pregnenolone, a 3β-hydroxy-5-ene and steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations and enriched in females compared to males. These findings lay the groundwork for mechanistic investigations into how microbial steroid metabolism modulates host hormonal physiology.}, } @article {pmid40625831, year = {2025}, author = {Han, Y and Ding, PH}, title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1616250}, pmid = {40625831}, issn = {2235-2988}, mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; }, abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.}, } @article {pmid40624949, year = {2025}, author = {Wu, M and Zhang, T and Han, S and Huan, S and Jiang, Y and Wang, Y and Cai, Z and Zhou, J}, title = {Structure and Function Features of Abundant and Rare Prokaryotic Communities Along Nearshore to Offshore Transitions.}, journal = {Environmental microbiology}, volume = {27}, number = {7}, pages = {e70144}, doi = {10.1111/1462-2920.70144}, pmid = {40624949}, issn = {1462-2920}, support = {42476137//National Natural Science Foundation of China/ ; KCXFZ20230731093402005//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; SGDX20220530111204028//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; RCJC20200714114433069//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; ZDSYS20230626091459009//Shenzhen Science and Technology Program of Shenzhen Science and Technology Innovation Bureau/ ; 2023KCXTD052//Innovation Team Project for Guangdong's Universities/ ; 2025A1515010643//Natural Science Foundation of Guangdong Province/ ; 2025A1515010519//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Biodiversity ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Microbiota ; Metagenome ; Metagenomics ; *Archaea/genetics/classification/isolation & purification ; }, abstract = {Abundant and rare taxa are crucial members of the marine microbial community. However, their biodiversity, assembly mechanisms, functional characteristics and ecological response strategies remain poorly understood. In this study, 16S rRNA and metagenomic sequencing were carried out to reveal the structural and functional features of abundant and rare taxa across the transition from nearshore to offshore. The results showed that the biodiversity of both abundant and rare taxa decreased with increasing distance from shore, with rare taxa exhibiting relatively higher diversity indices than abundant ones. Neutral model analysis revealed that the assembly process gradually changed from deterministic to stochastic from nearshore to offshore among abundant taxa. In contrast, among rare taxa, a stochastic process dominated nearshore, whereas a deterministic process was predominant in the offshore environment. Meanwhile, the proportion of variance that could be explained by environmental factors was relatively higher among abundant communities than among rare ones. A co-occurrence network analysis indicated that rare communities displayed greater complexity and a higher degree of modularity than abundant communities. Functionally, abundant communities tended to favour an r-strategy, whereas rare communities leaned towards a K-strategy. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns along coastal-to-open water transitions.}, } @article {pmid40624695, year = {2025}, author = {Li, Q and Huang, J and Zhou, Y and Wu, Q and Zhou, J and He, F and He, L and Shi, Y and Guo, C and Dai, J}, title = {Virome profiling of Aedes albopictus across urban ecosystems in Guangdong reveals sex-specific diversity.}, journal = {Parasites & vectors}, volume = {18}, number = {1}, pages = {264}, pmid = {40624695}, issn = {1756-3305}, support = {2024HK037//Scientific Research Project of General Administration of Customs/ ; 2024M760629//China Postdoctoral Science Foundation/ ; 2022YFC2302700//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Aedes/virology ; *Virome/genetics ; Female ; Male ; China ; *Mosquito Vectors/virology ; Phylogeny ; Ecosystem ; Metagenomics ; Cities ; Sex Factors ; Arboviruses/genetics/isolation & purification ; }, abstract = {BACKGROUND: Aedes albopictus mosquitoes are key vectors for arboviruses such as Dengue virus, Zika virus, and Chikungunya virus, posing significant global public health risks. Guangdong Province, a densely populated subtropical region in southern China, has experienced recurrent outbreaks of mosquito-borne diseases. However, sex- and geography-specific virome profiles of Aedes albopictus populations in this area remain uncharacterized, limiting the development of targeted surveillance strategies and precise risk assessment.

METHODS: We performed a metagenomic analysis of 1269 adult Aedes albopictus collected from five cities across Guangdong Province during autumn 2021. Mosquito pools underwent viral particle enrichment followed by DNA and RNA sequencing. Bioinformatic analyses were employed to characterize viral communities, evaluate alpha/beta diversity, and conduct phylogenetic reconstruction.

RESULTS: A comparative analysis of virome profiles in male and female Aedes albopictus across five regions of Guangdong Province (Chaozhou, Guangzhou, Shaoguan, Shenzhen, Zhanjiang) revealed significant viral distribution patterns influenced by both sex and geographic location. Female mosquitoes predominantly hosted vertebrate-associated arboviruses, including Flavivirus, consistent with their blood-feeding behavior. RNA virome composition showed significant sex-specific clustering (permutational multivariate analysis of variance, PERMANOVA, P = 0.008), with coastal cities (Shenzhen, Zhanjiang) being dominated by RNA viruses, whereas inland areas (Shaoguan) exhibited a predominance of DNA viruses. DNA virome profiles displayed divergence between sexes but marked regional variation. Guangzhou emerged as an outlier, exhibiting exceptional bacteriophage diversity distinct from other regions. Phylogenetic analysis identified zoonotic pathogens with signatures of cross-species transmission and region-specific evolutionary adaptation. These findings highlight the interplay between mosquito ecology, geographic factors, and viral evolution in shaping virome diversity.

CONCLUSIONS: This study presents the inaugural comparative analysis of DNA/RNA viromes in Aedes albopictus populations across Guangdong Province, revealing distinct sex-specific and geographic patterns in viral composition. The identification of vertebrate-associated viruses in female mosquitoes reinforces their epidemiological significance as arboviral vectors, while male-specific environmental viral signatures suggest potential pathways for ecological spillover. Coastal-inland and urban-rural disparities in viral communities emphasize the need for regionally tailored surveillance. These findings provide essential baseline virome data for forecasting emerging arboviral threats and informing strategies to mitigate zoonotic spillover in subtropical urban ecosystems.}, } @article {pmid40624638, year = {2025}, author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F}, title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {408}, pmid = {40624638}, issn = {1741-7015}, support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; }, mesh = {Animals ; *Dysbiosis/chemically induced/therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Diarrhea/chemically induced/microbiology/therapy ; Mice ; *Bacteroides fragilis ; Mice, Inbred C57BL ; *Probiotics/therapeutic use ; Mice, Inbred BALB C ; *Antineoplastic Agents/adverse effects ; Middle Aged ; Fluorouracil/adverse effects ; Feces/microbiology ; Female ; Aged ; }, abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.}, } @article {pmid40624612, year = {2025}, author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H}, title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.}, journal = {BMC gastroenterology}, volume = {25}, number = {1}, pages = {506}, pmid = {40624612}, issn = {1471-230X}, support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; }, mesh = {Humans ; *Cholangiocarcinoma/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; Male ; Middle Aged ; Female ; Metabolic Networks and Pathways ; *Dysbiosis/microbiology ; *Clostridiales/genetics/isolation & purification ; Aged ; Case-Control Studies ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.}, } @article {pmid40624564, year = {2025}, author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH}, title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {161}, pmid = {40624564}, issn = {2049-2618}, support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/isolation & purification/genetics/growth & development/metabolism ; *Microbial Interactions ; Coculture Techniques ; Metagenome ; Healthy Volunteers ; Feces/microbiology ; China ; }, abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.}, } @article {pmid40624535, year = {2025}, author = {Zhao, Y and Niu, X and Zhang, Y and Zhao, L and Zhang, L and He, J and Zhang, Q and Mao, Y and Wang, F and Zhao, X and Wang, R}, title = {Impact of supplementing Limosilactobacillus fermentum MN-LF23 on the eradication of Helicobacter pylori with 14-day standard quadruple therapy: a randomized, double-blind, placebo-controlled trial.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {106}, pmid = {40624535}, issn = {1475-2891}, support = {2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; 2022YFF1100100//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Male ; Female ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/therapy ; Double-Blind Method ; Middle Aged ; Adult ; *Limosilactobacillus fermentum ; Drug Therapy, Combination ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Dietary Supplements ; Dyspepsia ; }, abstract = {BACKGROUND: The effect of probiotics on Helicobacter pylori (Hp) infection demonstrates considerable heterogeneity. This study aims to elucidate the role of Limosilactobacillus fermentum MN-LF23 (MN-LF23) in Hp-infected populations.

METHODS: A total of 94 adult patients with confirmed Hp infection were enrolled in this study and randomly allocated to the placebo or MN-LF23 group. Patients initially received either placebo or probiotics along with standard quadruple therapy for 2 weeks, followed by continued administration of either placebo or probiotics for an additional 4 weeks. The eradication of Hp, serum levels of inflammatory factors, and alterations in gastrointestinal symptoms were assessed at weeks 0, 2, and 6, while fecal samples were collected for metagenomic sequencing.

RESULTS: The results showed no significant difference (P = 1) in the eradication rate between the placebo group (85.11%) and the probiotic group (82.98%). Following treatment, the incidence of constipation, dyspepsia, and Gastrointestinal Symptom Rating Scale (GSRS) scores in the probiotic group were markedly lower (P < 0.05) compared to those observed in the placebo group. Throughout the treatment process, there were no significant differences in TNF-α and IL-1β levels between the two groups. Compared to the placebo group, the probiotic group exhibited a significant increase in beneficial bacteria such as Limosilactobacillus fermentum, Lactiplantibacillus plantarum, Bifidobacterium longum, Coprococcus caltus, and Clostridium butyricum.

CONCLUSION: MN-LF23 supplementation did not improve the eradication rate of standard quadruple therapy. However, it significantly reduced the overall GSRS score, improved digestive and constipation symptoms, and promoted the proliferation of beneficial bacteria in the intestine.}, } @article {pmid40624250, year = {2025}, author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H}, title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24204}, pmid = {40624250}, issn = {2045-2322}, support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.}, } @article {pmid40624236, year = {2025}, author = {Wu, D and Niu, J and Hu, J and Wang, H and Kuang, H}, title = {Metabolomics combined with metagenomics analysis reveals the potential mechanism of Zhejiang psyllium polysaccharides against hyperuricemia in rats.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24180}, pmid = {40624236}, issn = {2045-2322}, mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism/chemically induced/blood/pathology ; *Metagenomics/methods ; *Metabolomics/methods ; Rats ; Uric Acid/blood ; Gastrointestinal Microbiome/drug effects ; Male ; *Psyllium/pharmacology/chemistry ; *Polysaccharides/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Kidney/pathology/drug effects/metabolism ; Blood Urea Nitrogen ; Creatinine/blood ; }, abstract = {This study aimed to assess the anti-hyperuricemia efficacy of Zhejiang psyllium polysaccharides (ZPP) in rats and to explore its underlying mechanism. Hyperuricemia was induced by intragastric administration of potassium oxonate, hypoxanthine, and adenine. The serum levels of uric acid (UA), creatinine (Cr), and blood urea nitrogen (BUN) were measured, and kidney pathology was examined. Serum metabolomics was employed to monitor metabolic alterations following ZPP intervention. Metagenomic analysis was conducted to investigate the impact of ZPP on the intestinal flora of hyperuricemia rats. The results showed that ZPP could significantly reduce the serum UA level in hyperuricemia rats and exhibited a certain renal protective effect. The metabolomics results indicated that ZPP regulates uric acid levels in rats with hyperuricemia and ameliorates renal pathological changes by modulating biomarkers associated with purine metabolism, amino acid metabolism, and lipid metabolism. Metagenomic research also found that ZPP could increase the relative abundance of uric acid metabolism-related probiotics, such as Limosilactobacillus reuteri and Lactobacillus murinus, thereby improving intestinal flora imbalance in rats with hyperuricemia.}, } @article {pmid40624115, year = {2025}, author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F}, title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24242}, pmid = {40624115}, issn = {2045-2322}, support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; }, mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; }, abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.}, } @article {pmid40624015, year = {2025}, author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M}, title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {130}, pmid = {40624015}, issn = {2055-5008}, support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; }, abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.}, } @article {pmid40621956, year = {2025}, author = {Huang, X and Yang, L and Zhou, S and Zhong, L and Xu, G and Bi, M and Yang, X and Su, X and Rillig, MC}, title = {Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates.}, journal = {Global change biology}, volume = {31}, number = {7}, pages = {e70329}, doi = {10.1111/gcb.70329}, pmid = {40621956}, issn = {1365-2486}, support = {42021005//National Natural Science Foundation of China/ ; U23A20145//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo Municipal Science and Technology Innovative Research Team/ ; ANSO-PA-2023-18//Alliance of International Science Organizations/ ; }, mesh = {*Biofilms/growth & development ; *Plastics ; *Nitrogen Cycle ; *Estuaries ; Transcriptome ; Nitrogen/metabolism ; Ecosystem ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; Metagenome ; }, abstract = {Biofilms represent a ubiquitous microbial lifestyle that facilitates colonization, symbiosis, and nutrient cycling, shaping environmental chemical transformations. In the Anthropocene, the proliferation of artificial surfaces, particularly plastics, has introduced novel and artificial ecological niches for microbial colonization. However, the biogeochemical potential of biofilms on these emerging artificial substrates remains largely unknown. Here, using [15]N tracing, amplicon, metagenome, and metatranscriptomic sequencing, we explore nitrogen (N) potential biogeochemistry across artificial and natural biofilms as well as the bulk seawater. Our results reveal that plastic biofilms exhibit enhanced N transformation potential, including elevated nitrification (2~45-fold), denitrification (5~44-fold), and N2O production (3~13-fold) rates, compared to natural biofilms and ambient seawater. This functional shift corresponds to distinct microbial community structures, driven by active N-cycling taxa and metabolic pathway reconfigurations on plastic surfaces. We also observe that carbohydrate metabolism pathways, such as glycolysis and the pentose phosphate pathway, were highly expressed in plastic biofilms, with transcriptional levels of glk (encoding glucokinase) and PGK (encoding phosphoglycerate kinase) increased by 6- and 2-fold, respectively. Our findings depict the role of plastic biofilms as active participants in estuarine N cycling and underscore the broader implications of plastic pollution on ecosystem biogeochemistry.}, } @article {pmid40621926, year = {2025}, author = {Samson, R and Kumar, S and Dastager, S and Khairnar, K and Dharne, M}, title = {Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0172024}, pmid = {40621926}, issn = {2165-0497}, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Rivers/microbiology/virology ; *Ice Cover/microbiology ; Humans ; Bacteriophages/classification/genetics/isolation & purification ; Geologic Sediments/microbiology ; Seasons ; }, abstract = {Glacier-fed rivers are significant ecological components of the river catchments, yet their microbial diversity and the associated antimicrobial potential remain underexplored. The Ganges is a glacier-fed river of immense cultural, religious, and ecological significance that supports over 400 million people downstream, providing essential water for agriculture, industry, and daily use. Despite its importance, the microbial community composition and antimicrobial potential, across its relatively pristine origin, remain largely underexplored. One possible explanation for this could be the lower microbial load in the upstream glacier-fed region, which likely results in a reduced DNA yield, insufficient for whole-metagenome sequencing, in contrast to the more biologically diverse and nutrient-rich lower reaches. In this study, we developed an efficient DNA extraction and amplification method using low-input DNA to sequence the microbiome from sediments of the glacier-fed Ganges River in pre-monsoon and post-monsoon over 2 years. Taxonomic and functional diversity of bacterial and viral (phage) communities were analyzed, together with the seasonal variations in their composition. Significant differences in microbial communities were observed in response to seasonal shifts (P < 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P < 0.05). The microbiome harbors potential for the biosynthesis of streptomycin, phenylpropanoid, penicillin, and cephalosporins. Bacteriophages from Podoviridae, Myoviridae, and Siphoviridae showed lytic potential against putrefying and pathogenic bacteria. This first comprehensive study on the glacier-fed Ganges River highlights significant seasonal shifts in microbial diversity. The initial insights into the functional profile of the bacterial and phage diversity offer opportunities to explore various natural compounds and enzymes to tackle antimicrobial resistance under the one-health canopy.IMPORTANCEThis study addresses a knowledge gap by exploring the microbial diversity and antimicrobial potential of the glacier-fed Ganges River across different seasons. The findings reveal various taxa with biosynthetic capabilities for antimicrobial compounds. Additionally, the presence of bacteriophages with lytic potential opens up opportunities for their exploration and application spanning various domains of one health. These findings lay a foundational basis for understanding the unique properties of this riverine ecosystem and offer valuable insights into environmental conservation and the potential to tackle antimicrobial resistance.}, } @article {pmid40619813, year = {2025}, author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT}, title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40619813}, issn = {1477-4054}, support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; }, abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.}, } @article {pmid40617811, year = {2025}, author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {228}, pmid = {40617811}, issn = {2158-3188}, mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; }, abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.}, } @article {pmid40616852, year = {2025}, author = {Zhu, X and Gao, X and Zhu, Y and Huang, J and Peng, F and Pang, Q and Yang, F and Xie, L and Hua, Z and Wang, L}, title = {The impact of land use on the composition of dissolved organic matter and its relationship with microbes in a river basin in Northwestern China: Insights into microbial community structure and metabolic function.}, journal = {Journal of environmental management}, volume = {391}, number = {}, pages = {126446}, doi = {10.1016/j.jenvman.2025.126446}, pmid = {40616852}, issn = {1095-8630}, mesh = {China ; *Rivers/microbiology ; Agriculture ; *Microbiota ; Bacteria/metabolism ; }, abstract = {Land use variations influence aquatic dissolved organic matter (DOM); however, the responses of relationships between DOM composition and microbial communities/metabolic genes to land use types and landscape indices remain insufficiently explored. This study conducted four field sampling sessions on the Qingshui River, northwestern China, investigated the shifts in DOM-transforming microbes and genes under distinct land use patterns (forest & grassland, urban area, and agricultural land) using metagenomics analysis, elucidated the DOM-microbe interactions in response to land use characteristics from the perspective of both basin and land use types by statistical approaches. At the basin scale, land use primarily influenced DOM quality rather than quantity. Partial least-squares path model demonstrated that landscape indices influenced DOM components predominantly by inhibiting gene abundances associated with metabolic pathways, exerting a more pronounced impact than land use area proportions. Notably, DOM composition, microbial metabolic genes, and their interactions differed significantly across land use types. Urban areas exhibited the highest levels of DOM aromaticity and the largest proportions of autochthonous sources, their fragmented landscape characteristics destabilized the microbial network, resulting in a comprehensive rather than partial suppression of genes involved in DOM transformation pathways (carbohydrate metabolism, energy metabolism, and amino acid metabolism). Compared to other land use scenarios, the downstream agricultural areas emerged as active zones for microbial utilization of DOM, maintained high microbial network stability and gene abundances similar to forest & grassland, highlighting the microbial resilience. These insights advance mechanistic understanding of how land use governs aquatic DOM-microbe interactions in arid and semi-arid watersheds.}, } @article {pmid40615957, year = {2025}, author = {Durand, K and Ogier, JC and Nam, K}, title = {The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {413}, pmid = {40615957}, issn = {1471-2180}, support = {ANR-10-LABX-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-001-01//Agence Nationale de la Recherche/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche,France/ ; Resistome//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification ; *DNA-Directed RNA Polymerases/genetics ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Computational Biology/methods ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Bacterial Proteins/genetics ; High-Throughput Nucleotide Sequencing/methods ; Shotgun Sequencing ; }, abstract = {BACKGROUND: The importance of microbial community profiling has been increasingly recognized in biological and environmental research. While metabarcoding has been widely used for such analysis by targeting specific DNA sequences as markers, shotgun sequencing has been proposed as an alternative method because the analysis of whole genomes can potentially reduce biases introduced by targeted approaches. However, it is largely unknown whether shotgun sequencing may provide improved precision for qualitative taxonomic identification and quantitative abundance estimation compared with metabarcoding with housekeeping gene markers, such as the rpoB gene. Furthermore, the comparative performance of various bioinformatics pipelines for shotgun data analysis remains uncertain. In this study, we evaluated the performance of rpoB metabarcoding and shotgun sequencing coupled to various bioinformatic pipelines to describe the bacterial diversity of artificially generated mock bacterial communities, which included eukaryote gDNA intentional contamination or whole-genome amplification. For shotgun sequencing, the Assembly-Binning-Method and k-mer-based approaches were evaluated.

RESULTS: For taxonomic profiling, the Assembly-Binning-Method and rpoB metabarcoding exhibited comparable sensitivity and precision, whereas k-mer approaches produced a notably high number of false negatives. In some cases, the Assembly-Binning-Method improved taxonomic resolution compared with rpoB metabarcoding by identifying taxa at the species level rather than the genus level. Regarding the quantification of microbial composition, the Assembly-Binning-Method consistently showed a higher correlation with expected values ​​and a lower dissimilarity index than rpoB metabarcoding. The use of three sets of reference genomes to calculate depth coverage did not systematically affect the precision of the Assembly-Binning-Method.

CONCLUSIONS: These results demonstrate that although shotgun sequencing and rpoB metabarcoding have nearly equivalent accuracy in taxonomic profiling, shotgun sequencing has better taxonomic resolution and outperforms rpoB metabarcoding in quantitative estimation of microbial community abundance using the Assembly-Binning approach.}, } @article {pmid40615853, year = {2025}, author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B}, title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {745}, pmid = {40615853}, issn = {1479-5876}, mesh = {Humans ; *Hepatic Encephalopathy/microbiology/etiology/blood ; *Liver Cirrhosis/microbiology/surgery/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; Ammonia/blood ; Aged ; }, abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.

RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.

CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.}, } @article {pmid40615598, year = {2025}, author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J}, title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23957}, pmid = {40615598}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; }, abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.}, } @article {pmid40615445, year = {2025}, author = {Di Gloria, L and Casbarra, L and Lotti, T and Ramazzotti, M}, title = {Testing the limits of short-reads metagenomic classifications programs in wastewater treating microbial communities.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23997}, pmid = {40615445}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Sewage/microbiology ; *Metagenome ; }, abstract = {Biological wastewater treatment processes, such as activated sludge (AS) and aerobic granular sludge (AGS), have proven to be crucial systems for achieving both efficient waste purification and the recovery of valuable resources like poly-hydroxy-alkanoates. Gaining a deeper understanding of the microbial communities underpinning these technologies would enable their optimization, ultimately reducing costs and increasing efficiency. To support this research, we quantitatively compared classification methods differing in read length (raw reads, contigs and MAGs), overall search approach (Kaiju, Kraken2, RiboFrame and kMetaShot), as well as source databases to assess the classification performances at both the genus and species levels using an in silico-generated mock community designed to provide a simplified yet comprehensive representation of the complex microbial ecosystems found in AS and AGS. Particular attention was given to the misclassification of eukaryotes as bacteria and vice versa, as well as the occurrence of false negatives. Notably, Kaiju emerged as the most accurate classifier at both the genus and species levels, followed by RiboFrame and kMetaShot. However, our findings highlight the substantial risk of misclassification across all classifiers and databases, which could significantly hinder the advancement of these technologies by introducing noises and mistakes for key microbial clades.}, } @article {pmid40613821, year = {2025}, author = {Saini, N and Ghosh, A and Bhadury, P}, title = {Linking plastic degradation potential and resistance gene abundance in bacterioplankton community of the Sundarbans estuarine ecosystem.}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf067}, pmid = {40613821}, issn = {1574-6968}, support = {DST/SJF/E&ASA-01/2017-18//Science and Engineering Research Board/ ; }, mesh = {*Bacteria/genetics/classification/metabolism/isolation & purification ; *Plastics/metabolism ; Biodegradation, Environmental ; Estuaries ; *Plankton/genetics/metabolism/classification ; India ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; }, abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.}, } @article {pmid40613581, year = {2025}, author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T}, title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40613581}, issn = {1477-4054}, support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; }, mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; }, abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.}, } @article {pmid40613164, year = {2025}, author = {Zhang, QL and Dong, LL and Zhang, LL and Wu, YJ and Li, M and Bo, J and Wang, LL and Jing, Y and Dou, LP and Liu, DH and Gu, ZY and Gao, CJ}, title = {[Characteristics of Gut Microbiota Changes and Their Relationship with Infectious Complications During Induction Chemotherapy in AML Patients].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {33}, number = {3}, pages = {738-744}, doi = {10.19746/j.cnki.issn.1009-2137.2025.03.017}, pmid = {40613164}, issn = {1009-2137}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/drug therapy/microbiology ; *Induction Chemotherapy ; Feces/microbiology ; Male ; Female ; Middle Aged ; }, abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota changes in patients with acute myeloid leukemia (AML) undergoing induction chemotherapy and to explore the relationship between infectious complications and gut microbiota.

METHODS: Fecal samples were collected from 37 newly diagnosed AML patients at four time points: before induction chemotherapy, during chemotherapy, during the neutropenic phase, and during the recovery phase. Metagenomic sequencing was used to analyze the dynamic changes in gut microbiota. Correlation analyses were conducted to assess the relationship between changes in gut microbiota and the occurrence of infectious complications.

RESULTS: During chemotherapy, the gut microbiota α-diversity (Shannon index) of AML patients exhibited significant fluctuations. Specifically, the diversity decreased significantly during induction chemotherapy, further declined during the neutropenic phase (P < 0.05, compared to baseline), and gradually recovered during the recovery phase, though not fully returning to baseline levels.The abundances of beneficial bacteria, such as Firmicutes and Bacteroidetes, gradually decreased during chemotherapy, whereas the abundances of opportunistic pathogens, including Enterococcus, Klebsiella, and Escherichia coli, progressively increased.Analysis of the dynamic changes in gut microbiota of seven patients with bloodstream infections revealed that the bloodstream infection pathogens could be detected in the gut microbiota of the corresponding patients, with their abundance gradually increasing during the course of infection. This finding suggests that bloodstream infections may be associated with opportunistic pathogens originating from the gut microbiota.Compared to non-infected patients, the baseline samples of infected patients showed a significantly lower relative abundance of Bacteroidetes (P < 0.05). Regression analysis indicated that Bacteroidetes abundance is an independent predictive factor for infectious complications (P < 0.05, OR =13.143).

CONCLUSION: During induction chemotherapy in AML patients, gut microbiota α-diversity fluctuates significantly, and the abundance of opportunistic pathogens increase, which may be associated with bloodstream infections. Patients with lower baseline Bacteroidetes abundance are more prone to infections, and its abundance can serve as an independent predictor of infectious complications.}, } @article {pmid40608492, year = {2025}, author = {Ozuru, R and Yamagishi, J and Takeuchi, A and Date, Y and Fujii, T and Sugimoto, C and Nakajima, C and Suzuki, Y and Aoki, K and Fujii, J and Matsuba, T}, title = {Unification of symbiotic bacteria during larva-to-adult transition in Culicoides circumscriptus (Diptera: Ceratopogonidae).}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf069}, pmid = {40608492}, issn = {1574-6968}, support = {24K13424//JSPS/ ; 18K16174//JSPS/ ; 21K16320//JSPS/ ; 24K10225//JSPS/ ; JP20wm0125008//Japan Agency for Medical Research and Development/ ; JP223fa62700//Japan Agency for Medical Research and Development/ ; }, mesh = {Animals ; *Ceratopogonidae/microbiology/growth & development ; Larva/microbiology/growth & development ; *Symbiosis ; Female ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Japan ; Microbiota ; Phylogeny ; }, abstract = {Blood-sucking midges such as Leptoconops and Culicoides are of medical importance due to their role in causing skin irritation and potentially transmitting pathogens. Investigating their bacterial communities, including possible endosymbionts, may help clarify ecological adaptations and interactions with hosts. Leptoconops nipponensis Tokunaga (Lnt) and Culicoides circumscriptus (Cc), blood-sucking midges, cause severe itching and inflammation in humans. Cc was collected from a small sample of an outbreak swarm of Lnt in the peninsula area of Yonago City, Tottori Prefecture, Japan. This study compared the bacterial flora of Lnt and Cc, revealing distinct bacterial diversity shifts in these insect species between life stages. We analyzed the bacterial communities of adult and larval females of Cc and Lnt using MiSeq sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Notably, alpha diversity in Cc adults was significantly reduced to 1.5 (n = 43), indicating that Cc adults were dominated by a single bacterial genus, compared to 14.9 in Cc larvae (n = 19). BLAST (Basic Local Alignment Search Tool) analysis identified this dominant genus in adult Cc as Rickettsia (Candidatus Tisiphisa), which is known for transovarial transmission in arthropod vectors. In contrast, the bacterial diversity of Lnt showed no significant difference between adults (18.1, n = 32) and larvae (n = 15). These findings suggest that the dominance of Rickettsia in Cc (Candidatus Tisiphisa) adults is linked to their emergence, potentially reflecting differences in reproductive biology and ecological adaptations between these two insect species. Further research is needed to elucidate the functional role of Rickettsia in the life cycle and physiology of Cc.}, } @article {pmid40607849, year = {2025}, author = {Zhang, H and Zhao, D and Wu, QL and Zeng, J}, title = {Environment selected microbial function rather than taxonomic species in a plateau saline-alkaline wetland.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {7}, pages = {e0220624}, pmid = {40607849}, issn = {1098-5336}, support = {U23A20153//National Natural Science Foundation of China/ ; BT2024012//Jiangsu Provincial Innovation Research Program on Carbon Peaking and Carbon Neutrality/ ; B240205024//Fundamental Research Funds for the Central Universities/ ; 2023YFF1304501//National Key R&D Program of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Wetlands ; *Soil Microbiology ; *Microbiota ; Salinity ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Methane/metabolism ; Nitrogen/metabolism ; Tibet ; Geologic Sediments/microbiology ; Metagenome ; Rhizosphere ; }, abstract = {UNLABELLED: Comprehending the microbial community in plateau saline-alkaline wetlands, an understudied and vulnerable ecosystem, is vital for predicting ecosystem functions within the context of global climate change. Despite the rapid shrinkage and potential drying up of some of these wetlands, our knowledge of the microbial community in this ecosystem remains fragmented. Here, we utilized metagenomic sequencing to investigate the distribution of methane, nitrogen, and sulfur cycling genes/pathways and formation mechanism of microbial communities across sediment, surface rhizosphere soils (Rsurface), subsurface rhizosphere soils (Rsubsurface), surface bulk soils (Bsurface), and subsurface bulk soils (Bsubsurface) in Cuochuolong Wetland, a typical saline-alkaline wetland located in the Tibetan Plateau. The results showed that sediment exhibited relatively higher functional potentials for methanogenesis but lower potentials for methane oxidation. Denitrification and dissimilatory sulfate reduction potentials increased with decreasing salinity across the five habitats, following the trend: sediment
IMPORTANCE: Understanding the formation mechanism of microbial communities is a central goal in ecology. However, our understanding of microbial community remains fragmented in plateau saline-alkaline wetlands, despite their unique status as a vulnerable ecosystem characterized by high altitude, low disturbance, high salinity, sensitivity to global climate change, and localized shrinkage in some areas. Furthermore, previous studies on community formation mechanism have predominantly focused on microbial taxonomic structure, neglecting their functional compositions. Beyond providing a comprehensive understanding of the distribution patterns of methane, nitrogen, and sulfur cycling microbial communities within plateau saline-alkaline wetland, this study offers a novel perspective on formation mechanism of microbial community by emphasizing the deterministic selection of extreme environment on microbial function. This study also expands our comprehension of the diversity of microbes containing the nod gene, which may substantially contribute to global methane and nitrogen budgets.}, } @article {pmid40607829, year = {2025}, author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB}, title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0038025}, pmid = {40607829}, issn = {2379-5077}, support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; T32 AI162579/AI/NIAID NIH HHS/United States ; K01-AI163413//National Institute of Allergy and Infectious Diseases/ ; ID #884//University of Maryland Baltimore Institute for Clinical & Translational Research/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; K01 AI163413/AI/NIAID NIH HHS/United States ; UH2 AI083264/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; *Vaginosis, Bacterial/drug therapy/microbiology/immunology ; *Metronidazole/therapeutic use/pharmacology ; *Vagina/microbiology/immunology/drug effects ; *Microbiota/drug effects ; Adult ; Biomarkers ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.}, } @article {pmid40604345, year = {2025}, author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB}, title = {Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {7}, pages = {e70417}, pmid = {40604345}, issn = {1552-5279}, support = {#ADSF-21-831381-C//AD Strategic Fund and the Alzheimer's Association/ ; R01AG083883/AG/NIA NIH HHS/United States ; #101053962//European Union's Horizon Europe research and innovation programme/ ; #2022-01018//Swedish Research Council/ ; //Olav Thon Foundation/ ; #2019-02397//Swedish Research Council/ ; U19 AG063744/AG/NIA NIH HHS/United States ; //Bluefield Project/ ; #ADSF-21-831377-C//AD Strategic Fund and the Alzheimer's Association/ ; S10 OD026929/OD/NIH HHS/United States ; U19AG063744/AG/NIA NIH HHS/United States ; #ADSF-21-831376-C//AD Strategic Fund and the Alzheimer's Association/ ; #FO2022-0270//Familjen Rönströms Stiftelse, Stiftelsen för Gamla Tjänarinnor, Hjärnfonden, Sweden/ ; #22HLT07//European Partnership on Metrology co-financed from the European Union's Horizon Europe Research and Innovation Programme and by the Participating States/ ; #201809-2016862//Alzheimer Drug Discovery Foundation (ADDF)/ ; R01 AG070973/AG/NIA NIH HHS/United States ; JPND2021-00694//European Union Joint Programme-Neurodegenerative Disease Research/ ; #ADSF-24-1284328-C//AD Strategic Fund and the Alzheimer's Association/ ; //Erling-Persson Family Foundation/ ; U01AG061359/AG/NIA NIH HHS/United States ; UKDRI-1003//NIH and Care Research University College London Hospitals Biomedical Research Centre and the UK Dementia Research Institute at UCL/ ; //Vilas Early-Career Investigator Award/ ; #ALFGBG-71320//Swedish State Support for Clinical Research/ ; U01 AG061359/AG/NIA NIH HHS/United States ; //Cure Alzheimer's Fund/ ; P30 AG062715/AG/NIA NIH HHS/United States ; #S10 OD026929/GF/NIH HHS/United States ; #2023-00356//Swedish Research Council/ ; R01AG070973/AG/NIA NIH HHS/United States ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie/ ; R01 AG083883/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Alzheimer Disease/microbiology/pathology/cerebrospinal fluid ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; Biomarkers/cerebrospinal fluid ; Feces/microbiology ; Metagenomics ; Amyloid beta-Peptides/cerebrospinal fluid ; Aged, 80 and over ; }, abstract = {BACKGROUND: The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.

METHODS: Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.

RESULTS: Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.

DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.

HIGHLIGHTS: Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) ε4 status+ vs APOE ε4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.}, } @article {pmid40604156, year = {2025}, author = {Kim, H and Nelson, P and Nzabarushimana, E and Shen, J and Jensen, J and Bhosle, A and Li, C and Lee, N and Everett, C and Berdy, B and Frongillo, G and Livny, J and Hu, FB and Simon, TG and McIver, L and Franzosa, EA and Chan, AT and Hayete, B and Thompson, KN and Huttenhower, C and Nguyen, LH}, title = {Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease.}, journal = {Nature metabolism}, volume = {7}, number = {7}, pages = {1476-1492}, pmid = {40604156}, issn = {2522-5812}, support = {R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35CA253185//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01 CA176726/CA/NCI NIH HHS/United States ; Research Professorship//American Cancer Society (American Cancer Society, Inc.)/ ; K23DK125838//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K23 DK125838/DK/NIDDK NIH HHS/United States ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32 CA009001/CA/NCI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; T32CA009001//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24 DK110499/DK/NIDDK NIH HHS/United States ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Female ; *Fatty Liver/microbiology/metabolism ; Metabolome ; Middle Aged ; Metagenome ; Adult ; Metagenomics ; Feces/microbiology ; Multiomics ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common condition linked to obesity and the metabolic syndrome, yet its transkingdom connections have been under-investigated. We performed high-resolution multi-omic profiling-including stool metagenomes, metatranscriptomes and metabolomes-in 211 MASLD cases and 502 controls from a cohort of female nurses. Here we show that MASLD is associated with shifts in 66 gut bacterial species, including widespread enrichment of oral-typical microbes, and transkingdom dysbiosis involving not only bacterial but also viral taxa. Streptococcus spp. are more abundant in non-lean versus lean MASLD, the latter being a paradoxical subtype of a disease typically associated with increased adiposity. These microbial changes correspond with shifts in transcripts and metabolites, including increases in polyamines and acylcarnitines and reductions in secondary bile acids. We highlight gut viral perturbations in MASLD, showing that expansions of bacteriophage targeting oral-typical bacteria correspond to expansions of their bacterial hosts in the gut. We provide a comprehensive resource for understanding MASLD and highlight transkingdom multi-omic microbial shifts as potential contributors to its aetiopathogenesis.}, } @article {pmid40604089, year = {2025}, author = {Das, B and Desai, M and Bhagora, NJ and Koringa, P and Pathan, M and Thakor, JC and Savaliya, FP and Adil, S and Hati, S}, title = {Influence of fermented whey protein fractions on the growth performance, haematological traits, serum biochemistry, faecal and caeca microbiota of broiler chickens.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23678}, pmid = {40604089}, issn = {2045-2322}, mesh = {Animals ; *Chickens/growth & development/microbiology/blood ; *Whey Proteins/pharmacology/metabolism ; *Feces/microbiology ; Fermentation ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; *Cecum/microbiology ; Male ; Limosilactobacillus fermentum/metabolism ; Female ; }, abstract = {Nowadays researchers and consumers are concerned about antibiotic resistance in poultry products causing antibiotic-resistant pathogens. Here, we investigated the effects of fermented whey peptides (FWP) with Limosilactobacillus fermentum (M4) as a nutraceutical supplement on growth performance, blood parameters, relative organs, and metagenomic analysis of broiler chickens, aiming to develop substitute for antibiotics in poultry feeds. An active culture of Lactobacillus fermentum (M4, GenBank Accession Number: MF951096) was inoculated into sterilized cheese whey at a rate of 2% (v/v) (10[7] CFU/ml) and incubated at 37 °C for 48 h. Ninety-six one-day-old mixed-sex commercial broiler chicks were randomly assigned in a Completely Randomized Design (CRD) experiment with four treatments, each having four replicates of six broiler chickens (6 × 4 × 4). One millilitre of liquid FWP fractions (> 10 kDa, < 10 kDa, and < 3 kDa) was freshly prepared and administered daily to the respective groups along with the basal diet from the 8th to the 15th day. Our current study revealed that supplementation with FWPs to broiler diets had no significant (p < 0.05) impact on body weight and FCR but numerically FCR value was high in control group. Blood cholesterol was significantly reduced in FWP fed groups. FWP had no significant impact on various blood parameters but influenced leukocytes and platelets. Metagenomic analysis showed no significant differences in microbial proportions. Histological analysis revealed no organ toxicity. The current findings suggest that broiler diets can substitute FWP for antibiotics to improve the growth performance and birds' health, without posing any biohazards. Furthermore, FWPs provide a variety of health benefits, potentially improving the health of humans who consume broiler meat or eggs.}, } @article {pmid40604039, year = {2025}, author = {Meng, K and Bao, Y and Chen, G and Qu, J and Liang, S and An, S and Chen, Y and Liu, X and Fu, X}, title = {Metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23298}, pmid = {40604039}, issn = {2045-2322}, support = {GNK2023ZX06//Guangxi Academy of Agricultural Science and Technology Development Project/ ; GK-AA22117015-3//the Guangxi Major Science and Technology Program/ ; GNK2021YT117//Guangxi Academy of Agricultural Sciences Basic Research Project/ ; 2019E016//Guangdong 3D Orthopedics Biomimetic Translational Medicine Engineering Technology Research Center/ ; }, mesh = {Animals ; *Aspartame/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Glioblastoma/pathology/genetics/microbiology ; Mice ; Disease Models, Animal ; *Metagenomics/methods ; Disease Progression ; Gene Expression Profiling ; *Transcriptome/drug effects ; *Brain Neoplasms/pathology/genetics/microbiology ; Humans ; Gene Expression Regulation, Neoplastic/drug effects ; Male ; Sweetening Agents/pharmacology ; }, abstract = {Aspartame, a widely used artificial sweetener, has been extensively studied for its potential health effects. Emerging evidence suggests that aspartame intake may directly impact the composition and function of the intestinal microbiota, which could subsequently influence the risk, progression, and treatment of glioblastoma multiforme (GBM) within the tumor microenvironment. However, it remains unclear whether aspartame intake affects intestinal flora, gene expression, and epigenetic regulation during tumor progression. To address these gaps in knowledge, we conducted a comprehensive metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model. Using a well-established mouse model and a rigorous metagenomics and transcriptomics approach, our results demonstrated that although the aspartame diet did not significantly affect tumor growth, it induced changes in the composition of the gut microbiota, particularly a decrease in the relative abundance of the Rikenellaceae family. Additionally, key N6-methyladenosine (m[6]A)-regulated genes, such as cyclin-dependent kinase inhibitor 1A (CDKN1A), MYC (myelocytomatosis) oncogene, and transforming growth factor-β (TGFB1), were significantly upregulated in GBM tumors exposed to aspartame. Notably, the expression of TGFB1 (transforming growth factor-β) suggested a critical role in the progression of GBM mediated by aspartame-induced m[6]A modifications. Our integrative analysis offered novel perspectives on the intricate interplay between dietary aspartame intake, gut microbiota, and tumor biology.}, } @article {pmid40603380, year = {2025}, author = {Wang, R and Wang, J and Wang, L and Cai, Y and Wang, Y and Luo, H and Chen, B and Chen, J and Fang, J and Song, Z}, title = {A novel eco-friendly Acinetobacter strain A1-4-2 for bioremediation of aquatic pollutants.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23207}, pmid = {40603380}, issn = {2045-2322}, support = {2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; }, mesh = {*Acinetobacter/metabolism/genetics/isolation & purification/classification ; *Biodegradation, Environmental ; Animals ; *Water Pollutants, Chemical/metabolism ; Zebrafish ; Phylogeny ; Metagenomics ; }, abstract = {The increasing accumulation of hydrocarbons and aromatic compounds in aquatic ecosystems, stemming from anthropogenic activities, poses severe ecological challenges, including disrupting biodiversity and threatening human health through the food chain. This study presents Acinetobacter strain A1-4-2, isolated from a hairy crab farming base, which could represent a novel Acinetobacter species. The metagenomic analysis of approximately 12,000 publicly available datasets revealed that this novel Acinetobacter species is widely distributed across various environments, particularly in those with high organic matter content, such as sludge, feces, and wastewater. Strain A1-4-2 exhibited exceptional metabolic capabilities, effectively degrading a diverse range of substrates, including amino acids, organic acids, oils, n-alkanes, lignin, and aromatic monomers. Genomic analysis, coupled with biological experiments, revealed that strain A1-4-2 exhibited resistance to a very limited kind of antibiotics. Moreover, the strain's biosafety, affirmed through zebrafish toxicity assays, underscores its suitability for environmental release. Additionally, the feasibility of genetic manipulation of strain A1-4-2 gives it the potential to become a chassis cell, enabling it to degrade organic pollutants more efficiently through genetic engineering. Our findings elucidate the strain's genomic and metabolic attributes, offering insights into its biodegradation potentials and developing effective strategies for ecological restoration in face of pollution.}, } @article {pmid40603374, year = {2025}, author = {Guta, M and Van Eenooghe, B and Bacha, K and Cools, P}, title = {Bacterial community profile of three Ethiopian hot springs based on 16S rRNA gene nanopore sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23491}, pmid = {40603374}, issn = {2045-2322}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; Ethiopia ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Nanopore Sequencing/methods ; Biodiversity ; }, abstract = {Ethiopia harbors a number of hot springs not yet well explored or studied using a metagenomic approach to reveal their bacterial diversity. Understanding the bacterial diversity of these ecosystems is valuable for uncovering their ecological roles and potential for biotechnological applications. The aim of this study was, therefore, to perform the first full-length 16S rRNA gene nanopore sequencing on the three Ethiopian hot springs, namely Shalla, Woliso and Wondo Genet. The bacterial community composition of the three hot springs, whose temperatures ranged from 45 to 96 °C, was effectively assessed using the ONT MinION sequencer. It was found that Shalla hot spring had the highest species richness and accounted for 323 species, followed by 116 species from Woliso and 54 species from Wondo Genet hot springs. Pseudomonadota and Bacillota were the most dominant phyla recovered from the three hot springs, whereas Acinetobacter and Paracoccus were the most abundant bacterial genera. The most abundant species were Alkalihalobacterium elongatum from Shalla hot spring, and Acinetobacter junii and Acinetobacter johnsonii from Wondo Genet hot spring. Our study provided the first insight into the bacterial diversity of three Ethiopian hot springs and may serve as a basis for further functional analysis of these hot springs.}, } @article {pmid40603287, year = {2025}, author = {Samarra, A and Alcañiz, AJ and Martínez-Costa, C and Marina, A and Comas, I and Segata, N and Quijada, NM and Collado, MC}, title = {Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6099}, pmid = {40603287}, issn = {2041-1723}, support = {MAMI-639226 project//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; PROMETEO2020/12//Generalitat Valenciana (Regional Government of Valencia)/ ; CIPROM2023/030//Generalitat Valenciana (Regional Government of Valencia)/ ; }, mesh = {Humans ; *Breast Feeding ; *Bifidobacterium/physiology/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Cesarean Section ; Metagenome ; Adult ; Male ; Milk, Human/microbiology ; Feces/microbiology ; }, abstract = {The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, we identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.}, } @article {pmid40602621, year = {2025}, author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X}, title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70139}, pmid = {40602621}, issn = {1758-2229}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.}, } @article {pmid40602565, year = {2025}, author = {Rajeswari, G and Kumar, V and Jacob, S}, title = {Advanced lignocellulose bioprocessing for Aloe vera leaf rind through novel termite gut microbiome consortia for acetone butanol ethanol (ABE) production: Metagenomics insights and process economic analysis.}, journal = {International journal of biological macromolecules}, volume = {319}, number = {Pt 4}, pages = {145691}, doi = {10.1016/j.ijbiomac.2025.145691}, pmid = {40602565}, issn = {1879-0003}, mesh = {*Lignin/metabolism/chemistry ; Animals ; *Gastrointestinal Microbiome ; *Isoptera/microbiology ; *Ethanol/metabolism ; *Plant Leaves/chemistry/metabolism ; *Aloe/chemistry ; *Metagenomics/methods ; *Acetone/metabolism ; *Butanols/metabolism ; Biomass ; *Microbial Consortia ; }, abstract = {Consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) using microbes simplifies the process, eliminates enzyme cost and reduces the overall processing expenses. In this regard, termite gut, a potent reservoir of microbial symbionts produces various lignocellulolytic enzymes which acts synergistically to degrade LCB. However, the effectiveness of adapting the microbes with LCB for improved lignocellulolytic enzyme secretion and substrate degradation in a biorefinery framework has been overlooked. Hence, in this study adaptive laboratory evolution (ALE) of termite gut isolates was performed with various substrates such as saw dust (SD) and Aloe vera leaf rind (AVLR) under different conditions. Among the consortia, enriched termite consortium (ETC-3) showed the highest degradation of lignin (51.86 ± 2.03%, w/w), hemicellulose (29.27 ± 1.29%, w/w) and cellulose (41.97 ± 2.99%, w/w) with maximum specific enzyme activities. High throughput sequencing revealed the significant enrichment of Proteobacteria (88.95%) and Ascomycota (99.94%) groups in ETC-3. Further, the efficiency of ETC-3 in consolidated pretreatment and bioprocessing (CPBP) and CBP of AVLR towards acetone, butanol and ethanol (ABE) production was studied. Compared to the CPBP, CBP resulted in 1.6-fold higher glucose yield which subsequently enhanced the butanol yield (7.97 ± 0.40 g/L). Finally, cost-benefit analysis ensured the economic feasibility of process strategies for AVLR valorization.}, } @article {pmid40601719, year = {2025}, author = {Wanjiru, T and Bulimo, W and Langat, S and Kinyua, J and Odemba, N and Yalwala, S and Oullo, D and Ochieng, R and Ngere, F and Kerich, G and Ambale, J and Achieng, E and Abuom, D and Egbo, T and Johnson, J and Ojwang, E and Eads, J and Garges, E and Eyase, F}, title = {Vertical transmission of Dengue virus type-3 and metagenomic virome profiles of Aedes aegypti mosquitoes collected in Kisumu, Kenya.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0315492}, pmid = {40601719}, issn = {1932-6203}, mesh = {Animals ; *Aedes/virology ; Kenya ; *Dengue Virus/genetics/isolation & purification/classification ; *Virome/genetics ; *Mosquito Vectors/virology ; *Infectious Disease Transmission, Vertical ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Dengue/transmission/virology ; Metagenome ; Female ; }, abstract = {Aedes aegypti is the main vector of several arboviruses including chikungunya, dengue, yellow fever and Zika. Beyond arboviruses, Aedes aegypti harbours insect-specific viruses (ISVs), which can modulate mosquito's ability to transmit diseases by interfering with viral processes and triggering immune responses. Both arboviruses and ISVs can be transmitted vertically, where viruses are passed from parent to offspring. The lack of systematic molecular and entomological surveillance, has left the diversity of viruses in local Aedes aegypti populations largely unexplored. This study aimed to characterize the viromes of Aedes aegypti mosquitoes from Kisumu, Kenya, focusing on viral diversity. Immature larvae and pupae were collected from Jua Kali area in Kisumu, reared into adults, and subjected to viral isolation by cell culture and metagenomic next-generation sequencing. RNA extraction, library preparation, and Illumina MiSeq sequencing were performed on CPE positive pools and metagenomic superpools. Initial data analysis was conducted using the CZ-ID platform, with quality control applied using PrinseqLite v0.20.4 to filter low-quality reads and remove adapters. De novo sequence assembly was performed with MEGAHIT v1.2.9, followed by BLAST analysis. Phylogenetic relationships were analyzed using the Maximum Likelihood method. A total of 2,142 female Aedes aegypti, grouped into 86 pools and 4 superpools, were analyzed using cell culture and metagenomic next-generation sequencing respectively. Dengue virus type-3 was detected in one of the 86 pool. Additionally, a variety of ISVs were identified, including Iflaviruses related to Tesano Aedes Iflavirus (TeAV), Armigeres Iflavirus, and Negeviruses related to Rabai Virus. An unclassified virus closely related to Korle-Bu Aedes virus was also detected. Our study provides insights into the viral diversity within Aedes aegypti mosquitoes in Kisumu and evidence of natural vertical transmission, specifically transovarial transmission of dengue virus type-3. Ongoing research is imperative to unravel vertical transmission mechanisms and subtleties governing ISV-arbovirus interactions across diverse environmental settings.}, } @article {pmid40601568, year = {2025}, author = {Manavalan, S and Pradeep, D and Dharmalingam, D and Semalaiyappan, J and Sivarasan, T and Venkatesan, S and Thirumal, S and Kuttiatt, VS}, title = {Comparative analysis of skin microbiome of patients with filarial lymphedema and healthy individuals.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0325380}, pmid = {40601568}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; Male ; *Skin/microbiology ; *Elephantiasis, Filarial/microbiology ; Adult ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Lymphedema/microbiology ; Pilot Projects ; Skin Microbiome ; }, abstract = {BACKGROUND: Lymphatic filariasis, a vector borne parasitic disease is a public health problem in the tropical region. Recurrent skin and soft tissue infections termed adenolymphangitis (ADL) is a major complication of filarial lymphedema. Understanding the changes in skin microbiome associated with this disease may provide novel insights on ADL attacks and lymphedema progression. This study investigates the changes in skin microbial flora in patients affected with filarial lymphedema.

METHODS: We employed 16S rRNA gene amplicon-based metagenomic technique to profile the skin microbiome of patients with filarial lymphedema in comparison with healthy volunteers.

RESULTS: There were notable differences in the bacterial flora between patients and healthy controls. Actinobacteria were under-represented in the patient group. Staphylococcus dominated both the groups, 63% in patients and 44% in controls. Samples from a few patients showed the presence of certain rare bacteria like Eremococcus and Facklamia.

CONCLUSION: This pilot study applying advanced molecular tools provides insight on the changes in skin microflora associated with filarial lymphedema for the first time. Further studies are necessary for a better understanding of the role of the altered skin microbiome in frequent episodes of adenolymphangitis in patients with filarial lymphedema.}, } @article {pmid40600714, year = {2025}, author = {Li, Y and Sun, C and Zhu, J and Geng, M and Li, M and Zhao, X-M and Chen, W-H}, title = {Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0001325}, pmid = {40600714}, issn = {2165-0497}, support = {Nos. 32070660//National Natural Science Foundation of China/ ; T2225015,61932008//National Natural Science Foundation of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Genome, Viral ; Feces/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; Infant ; Adult ; Metagenome ; Female ; Male ; }, abstract = {UNLABELLED: Due to varying sequencing strategies, current gut virome findings show significant variability. Specifically, bulk- and virus-like particle (VLP)-enriched metagenomic sequencing (termed bulk and VLP, respectively) present unique advantages and limitations, affecting viral genome discovery, taxonomic annotation, and community structure analysis. A comprehensive comparison of these strategies is crucial for thoroughly understanding the gut virome. This study comprehensively compared gut viromes identified from paired bulk and VLP data from 151 adult and 141 infant fecal samples. The VLP method showed superior performance to bulk in viral genome discovery in both data sets by recovering longer and more complete viral genomes, with higher sensitivity for low-abundant ones, resulting in a higher taxonomic annotation rate. However, we observed no correlations in the viral community structure (i.e., Shannon diversities) between bulk- and VLP-derived viromes, implying biases introduced during VLP enrichment. Such biases could be caused by the bacterial host features, such as the structural differences in cell walls and the prevalence and abundance of the viruses. Viruses that are of low prevalence, low abundance, or have Gram-positive bacteria as their hosts were enriched in VLP-derived viromes, in both the adult and infant data sets. Significant complementarity was observed between bulk and VLP viromes, with only about a quarter (26.7% in infants; 29.3% in adults) of VLP-viral genomes overlapping with bulk viruses. Together, our study identifies causal factors underlying the biases of bulk and VLP strategies in human gut virome studies and advocates the use of both strategies to enhance a comprehensive understanding of gut viromes.

IMPORTANCE: The two mainstream gut phageome profiling strategies, namely bulk and virus-like particle (VLP), generated significantly overlapped results and have their own merits and drawbacks. Particularly, VLP exhibits higher efficiency in obtaining more, longer, and more complete viral genomes. However, VLP sequencing has the potential to alter the natural structure of viral communities, often resulting in the identification of viruses with lower prevalence and those specifically associated with Gram-positive bacterial hosts. While bulk metagenome features a more stable and diverse community, which can well reveal the interactions between viruses and bacteria. Nevertheless, bulk sequencing can suffer from lower coverage, leading to fragmented sequences and potentially missing some viral species. Therefore, it is essential to recognize that these methods are complementary rather than competitive in the comprehensive characterization of the gut phageome.}, } @article {pmid40600712, year = {2025}, author = {Comeault, AA and Orta, AH and Fidler, DB and Nunn, T and Ellison, AR and Anspach, TA and Matute, DR}, title = {Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0002725}, pmid = {40600712}, issn = {2379-5077}, support = {R35 GM148244/GM/NIGMS NIH HHS/United States ; RGS\R1\221323//Royal Society/ ; R35GM148244/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Phylogeny ; *Metagenome/genetics ; *Drosophila/microbiology/genetics ; *Bacteria/genetics/classification ; *Genome, Bacterial ; Gastrointestinal Microbiome/genetics ; Microbiota ; }, abstract = {Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (Drosophila). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.}, } @article {pmid40599650, year = {2025}, author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA}, title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1522970}, pmid = {40599650}, issn = {2235-2988}, mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.

OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.

METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.

RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.

CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.

CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.}, } @article {pmid40598608, year = {2025}, author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW}, title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.}, journal = {Veterinary research}, volume = {56}, number = {1}, pages = {133}, pmid = {40598608}, issn = {1297-9716}, support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; }, mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; }, abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.}, } @article {pmid40598319, year = {2025}, author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C}, title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {155}, pmid = {40598319}, issn = {2049-2618}, support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; }, mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.

CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.}, } @article {pmid40597620, year = {2025}, author = {Yang, L and Yan, Y and Shen, J and Xia, Y and Lang, F and Chen, C and Zou, W}, title = {Metagenomic insights into microbial community succession and its functional changes during the stage of acetic acid fermentation of shanxi aged vinegar.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {374}, pmid = {40597620}, issn = {1471-2180}, support = {20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; }, mesh = {*Acetic Acid/metabolism ; Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Acetobacter/metabolism/genetics ; Metabolic Networks and Pathways ; *Microbiota/genetics ; Food Microbiology ; Metagenome ; }, abstract = {Traditional fermentation of Shanxi aged vinegar involves complex microbial interactions driving flavor synthesis, but the mechanisms underpinning metabolic adaptation and community succession remain poorly characterized. This study aimed to unravel stage-specific microbial dynamics and their functional contributions to flavor formation during Cupei fermentation. Metagenomic sequencing analyzed microbial communities and metabolic pathways at three fermentation stages (D3, D6, D9). Functional annotation (KEGG, CAZy) and species-level contribution assessments identified key taxa and genes linked to flavor biosynthesis. Microbial succession shifted from Lactobacillus dominance (64.68% at D3) to Acetobacter prevalence (48.04% at D9), with Lactobacillus acetotolerans persisting throughout (17.15-26.23%). Early-stage carbohydrate metabolism (GHs-driven: 60.38% at D3) transitioned to late-stage amino acid (15.62%) and cofactor synthesis (12.17%), activating valine, leucine, and histidine pathways critical for flavor compounds. Acetobacter oryzoeni and Acetobacter pomorum drove acetate (ALDH: 27.07-41.52%), valine (ilvE: 53.21-20.22%), and histidine (hisD: 41.83-33.30%) metabolism at D9. Low abundance species (Weissella confusa, 0.51%) and uncultured Limosilactobacillus sp. contributed via multi-gene networks (e.g., dat, ldh), which revealed an important functional contribution by overlooked low-abundance species. The study uncovers ecological coupling between microbial succession and metabolic adaptation, where dominant taxa and rare species synergistically govern flavor formation. These insights enable targeted microbial community design for flavor optimization in traditional fermented foods.}, } @article {pmid40597414, year = {2025}, author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R}, title = {Microbiome-based therapeutics towards healthier aging and longevity.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {75}, pmid = {40597414}, issn = {1756-994X}, mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; }, abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.}, } @article {pmid40597307, year = {2025}, author = {Wang, Z and Wang, W and Wang, Y and Hu, H and Wang, B and Zhu, W and Li, X and Hou, X and Sun, W and Liu, Z and Lu, S and Chen, X}, title = {Mapping gut microbiota and metabolite alterations in patients with postmenopausal osteoporosis in the Beijing Community of China.}, journal = {European journal of medical research}, volume = {30}, number = {1}, pages = {539}, pmid = {40597307}, issn = {2047-783X}, support = {No.2020YFC2004900//National Key Research and Development Program of China/ ; H0608//National Natural Science Foundation of China/ ; No.81672201, 81871794//Natural Science Foundation of China/ ; No.7242065//Beijing Natural Science Foundation/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology ; Middle Aged ; Aged ; Bone Density ; Beijing ; China ; Feces/microbiology ; }, abstract = {INTRODUCTION: Postmenopausal osteoporosis (PMO) is a chronic disease in the elderly women, which has been shown to be related to the gut microbiota (GM) alternation in recent studies. Few studies have investigated which specific bacterial species and metabolites have an impact on postmenopausal osteoporosis patients, especially in urban communities.

METHODS: With the aim of comprehending GM features and metabolite variation in women suffering from PMO in the Beijing Community of China, we divided the 76 eligible participants into osteoporosis (OP) and health control (HC) groups taking into account the bone mineral density (BMD), and adopted 16 S rRNA gene sequencing and metagenomic sequencing to examine the GM compositions in the respective groups. Besides, the study adopted liquid chromatography and mass spectrometry (LC-MS) for the fecal metabolite analysis.

RESULTS: The OP group presented obviously changed bacterial α-diversity and β-diversity versus the HC group. GM at the genus level was differentially enriched in the OP or HC groups. Megamonas genus exhibited the strongest positive relevance to BMD and OC. Bacteroides genus had the strongest negative relevance to BMD and positive relevance to β-CTX. GM at the species level was also differentially enriched in OP or HC groups. After multiple linear regression analysis, Roseburia_intestinalis and Glycoursodeoxycholic acid were positively associated with BMD, hinting their beneficial effect in BMD. Corresponding signaling pathways also exhibited an obvious change, particularly in up-regulation Glycerol Phosphate Shuttle and down-regulation Malate-Aspartate Shuttle pathways.

CONCLUSIONS: According to the results of this study, GM and metabolites in women with PMO in the Beijing Community changed dramatically, which were significantly associated with BMD and bone turnover markers. Roseburia_intestinalis and Glycoursodeoxycholic acid levels were the most positively associated with BMD. All these assist in understanding the development mechanism of PMO from new perspectives and in developing novel therapeutic methods for improving bone health.}, } @article {pmid40596882, year = {2025}, author = {Hekker, MD and Platteel, TN and Venekamp, RP and Top, J and Geerlings, SE and Schultsz, C and de Vos, MGJ and van de Wijgert, JHHM}, title = {Urinary tract infections in postmenopausal women revisited (UTIr): a prospective observational cohort study to explore the urobiomes of postmenopausal women with and without recurrent urinary tract infections.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {822}, pmid = {40596882}, issn = {1471-2334}, support = {OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; }, mesh = {Humans ; Female ; *Urinary Tract Infections/microbiology/epidemiology ; *Postmenopause ; Prospective Studies ; Middle Aged ; Recurrence ; Vagina/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Recurrent urinary tract infections (RUTI) are prevalent, particularly among postmenopausal women, and place a significant burden on the affected individuals and the healthcare system. While Escherichia coli is the primary cause of most UTIs in premenopausal women, this may not hold true for postmenopausal women. To facilitate development of novel diagnostics, preventive interventions, and clinical management of RUTI in postmenopausal women, it is essential to strengthen the biological evidence base.

METHODS: This observational prospective cohort study will enrol 20 postmenopausal women without RUTI (controls) and approximately 30 with RUTI (cases), aiming to sample at least 50 UTI episodes. Questionnaires are completed, samples (urine, vulvoperineal and vaginal swabs, and faeces) are collected by participants or study staff at five scheduled time points over one year of follow-up, as well as during and after each UTI episode. All samples will undergo 16S rRNA amplicon sequencing, with selected urine samples also subjected to bacterial culturing, metagenomic sequencing, and metabolomics. Various urobiome comparisons will be conducted, such as between women with and without RUTI in the absence of a UTI, and over time during UTIs. Urobiomes will also be compared to vaginal, vulvoperineal, and gut microbiomes in the same women at the same time points. Finally, urine samples will be cultured to obtain bacterial isolates, which will be characterised and used for co-culture and urothelium organoid experiments.

DISCUSSION: The UTIr cohort study is an exploratory, hypothesis-generating study designed to improve understanding of the ecological mechanisms driving UTI onset, response to antibiotic treatment, and UTI recurrence in postmenopausal women. The data collected from each individual woman is longitudinal and comprehensive, which is instrumental for advancing the field. The study population consists of women over the age of 50 and the study procedures are demanding. Flexibility with protocol procedures has proven to be essential to maximise retention and minimise missing data. We recommend employing a sufficiently large recruitment team and/or planning for a sufficiently long recruitment period to accommodate the demanding nature of these types of in-depth studies with vulnerable populations.

TRIAL REGISTRATION: Not applicable.}, } @article {pmid40596159, year = {2025}, author = {Bayatian, M and Pourbabaee, AA and Amoozegar, MA}, title = {Revealing the composition of bacterial communities in various oil-contaminated soils and investigating their intrinsic traits in hydrocarbon degradation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22016}, pmid = {40596159}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Petroleum/metabolism ; Soil/chemistry ; *Microbiota ; Petroleum Pollution ; Iran ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {This study explores prokaryotic diversity and oil biodegradation potential in soils from three evaporation ponds in the Ahvaz and Maroon oil fields, Iran. Despite prior studies on prokaryotic diversity in contaminated soils, systematic comparisons within the same region remain limited. The analysis identified distinct physicochemical differences across sites. Ahvaz 1 soil, with a loamy silty clay texture, had the highest salinity (15.4%) and total petroleum hydrocarbons (TPH, 3.5%). Ahvaz 4 soil, loamy silty in texture, showed 7.49% salinity and 1% TPH, while Maroon 3 soil exhibited the lowest salinity (5.06%) and TPH (0.5%). Prokaryotic diversity and biodegradation traits were assessed using 16S rRNA next-generation sequencing (NGS) and qPCR, respectively. NGS revealed reduced prokaryotic diversity in all contaminated soils, with Bacillota dominating, whereas Pseudomonadota prevailed in all control samples. Maroon 3 soils had higher diversity, but Cyanobacteria and Actinomycetota, dominant in controls, were replaced by Chloroflexota, Gemmatimonadota, and Acidobacteriota in polluted soils. At the genus level, Bacillus, Lysinibacillus, Virgibacillus, Brevibacillus, and Paenibacillus showed increased abundance in contaminated soils. Real-time PCR of alkB and C23DO genes indicated enhanced hydrocarbon degradation potential. FAPROTAX and PICRUSt2 analyses revealed enhanced microbial capacity for hydrocarbon degradation in polluted soils, with enriched functions related to chemoheterotrophy, aromatic compound degradation, and increased levels of alkane 1-monooxygenase, alcohol dehydrogenase, and protocatechuate 4,5-dioxygenase subunits. The findings highlight crude oil's impact on microbial community structure, reducing archaea and emphasizing bacterial dominance while underscoring shifts in microbial responses and functional gene expression in hydrocarbon degradation.}, } @article {pmid40595658, year = {2025}, author = {Zhang, Z and Liu, Y and Zhao, W and Liu, K and Chen, Y and Wang, F and Mao, G and Ji, M}, title = {Distinct genes and microbial communities involved in nitrogen cycling between monsoon- and westerlies-dominated Tibetan glaciers.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5926}, pmid = {40595658}, issn = {2041-1723}, support = {42421001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42330410//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20176//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Tibet ; *Nitrogen Cycle/genetics ; *Ice Cover/microbiology ; *Microbiota/genetics ; Nitrogen/metabolism ; Metagenome/genetics ; Climate Change ; Bacteria/genetics/metabolism/classification ; Temperature ; Nitrous Oxide/metabolism ; Nitrogen Fixation/genetics ; Transcriptome ; }, abstract = {The Tibetan Plateau (TP) glaciers are influenced by monsoon and westerlies. They are highly sensitive to climate change, with atmospheric nitrogen deposition significantly impacting microbial communities and functions. However, key uncertainties persist regarding biogeography and drivers of genes and microbial communities involved in nitrogen cycling. Here, we investigate the diversity and transcriptional activity of microbial communities and nitrogen-cycling genes using 85 metagenomes and 28 metatranscriptomes from the ablation zone of 21 TP glaciers. Our results show that over 90% of the glacial taxa possess the potential for nitrogen metabolism, with ~33% exhibiting transcriptional activity. Moreover, monsoon-dominated glaciers present greater microbial diversity and higher prevalence of nitrogen-fixing genes than westerlies-dominated glaciers, linked to higher temperatures. Comparatively, the latter show elevated genomic potential for nitrous oxide emissions, likely due to higher nitrate concentrations. These findings establish temperature-nitrogen co-regulation of microbial nitrogen transformations, critical for predicting climate feedback in the extreme environment.}, } @article {pmid40595444, year = {2025}, author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B}, title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {970}, pmid = {40595444}, issn = {2399-3642}, support = {R35 GM155208/GM/NIGMS NIH HHS/United States ; 1R35GM155208-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; }, abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.}, } @article {pmid40595004, year = {2025}, author = {Raina, TK and Gupta, M and Salgotra, RK}, title = {Metagenomic analysis to identify unique microbes in the rhizosphere of basmati rice (Oryza sativa L.) accessions.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22864}, pmid = {40595004}, issn = {2045-2322}, mesh = {*Oryza/microbiology/genetics ; *Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Odorants/analysis ; Microbiota ; }, abstract = {The captivating aroma of basmati rice is highly favoured by consumers across the globe. Unfortunately, the aroma of basmati rice has been gradually diminishing over time due to the excessive use of inorganic fertilizers and the impact of climate change. To understand the microbial community that plays a significant role in aroma enhancement in basmati rice accessions, a systematic study is required. A unique rhizobacteria of basmati rice associated with basmati rice were Actinobacteria, Bacillus subtilis, Burkholderia, Enterobacter, Klebsiella, Lactobacillus, Micrococcus, Pseudomonas, and Sinomonas. The biosynthesis of potential precursors (ornithine, putrescine, proline, and polyamines) of aroma in basmati rice involved various enzymes such as acetylornithine aminotransferase, acetylornithine deacetylase, N-acetylornithine carbomyltransferase, acetylornithine/succinyldiaminopimelate aminotransferase, and ornithine cyclodeaminase. These findings significantly contribute to the existing understanding of the rhizobacteria associated with basmati rice that play a crucial role in enhancing the aroma. The introduction of these cultures into the basmati rice growing areas has the potential to augment the plant growth and enhances the aroma. The present study explored the functional potential of the microbial community associated with aroma improvement in basmati rice. This will also enhance the export potential of the basmati rice in the region on sustainable basis.}, } @article {pmid40594354, year = {2025}, author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO}, title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22448}, pmid = {40594354}, issn = {2045-2322}, support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; }, abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.}, } @article {pmid40594317, year = {2025}, author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D}, title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20549}, pmid = {40594317}, issn = {2045-2322}, support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; }, abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.}, } @article {pmid40593979, year = {2025}, author = {Chen, L and Chen, H and Lv, T and Guo, X and Wu, W and Zhao, D and Liu, F}, title = {Differences of the respiratory microbiota between children suffering from community acquired pneumonia with presence or absence of asthma.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20458}, pmid = {40593979}, issn = {2045-2322}, mesh = {Humans ; *Asthma/microbiology/complications ; *Community-Acquired Infections/microbiology/complications ; *Microbiota ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia/microbiology/complications ; Infant ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Adolescent ; Community-Acquired Pneumonia ; }, abstract = {Recent advancements in respiratory microbiota research have progressively elucidated their pivotal role in pediatric respiratory pathologies. Alterations in airway microbial communities are intricately associated with diverse respiratory conditions and distinct disease states. This study conducted a comparative analysis of respiratory microecological profiles in pediatric cohorts diagnosed with community-acquired pneumonia (CAP), stratified by the presence or absence of comorbid bronchial asthma, from whom nasopharyngeal aspirates were obtained for metagenomic next-generation sequencing (mNGS). Analyses revealed comparable alpha-diversity indices between groups; however, beta-diversity metrics demonstrated marked compositional divergence. In the asthma-CAP cohort, Streptococcus pneumoniae and Rothia mucilaginosa emerged as predominant taxa, whereas Mycoplasmoides pneumoniae and Trichoderma citrinoviride dominated microbial profiles in uncomplicated CAP patients.}, } @article {pmid40593735, year = {2025}, author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC}, title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {121}, pmid = {40593735}, issn = {2055-5008}, support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovación/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovación/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 898088//European Union's Horizon 2020/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; /WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; 639226/ERC_/European Research Council/International ; }, mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; }, abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.}, } @article {pmid40593262, year = {2025}, author = {Liu, L and Li, M and Qin, Y and Liu, Y and Li, M and Lian, B and Guo, R and Xiao, Y and Yin, C}, title = {Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21436}, pmid = {40593262}, issn = {2045-2322}, support = {81903340//National Natural Science Foundation of China/ ; }, mesh = {Child ; Female ; Humans ; Male ; *Blood Proteins/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Metagenomics/methods ; *Pediatric Obesity/microbiology/blood/metabolism ; Proteomics/methods ; }, abstract = {The aim of this study was to investigate the changes in the gut microbiota and proteins related to metabolism and immunity caused by childhood obesity and insulin resistance (IR) and to assess the underlying relationship between the gut microbiota and IR in children. Nineteen children with obesity and sixteen healthy children were recruited. Children with obesity were divided into two groups: obese with IR and obese without IR. All of the obese children participated in a 1-month lifestyle-based weight loss program. Faecal metagenomics and serum Olink proteomics combined with clinical parameters were used to identify the metabolic alterations associated with childhood obesity and IR. The gut microbiota and serum protein were significantly altered in obese children with IR. The relative abundances of Akkermansia muciniphila, IGFBP1 and GP6 were decreased in obese children with IR. Butyricicoccus sp. AM29-23AC, DLK1, CD163, CCL16 and CTSD levels were recovered after IR improved. TNFR1 had a significant indirect effect on the interaction between s-Citrobacter.freundii and fasting insulin. In conclusion, obese children with IR have abnormal gut microbiota and serum proteins related to metabolism and immunity, which can be improved after weight loss. The gut microbiome of children with obesity may contribute to the development of IR by triggering metabolic inflammation.Clinical Trial Registration: This study was registered with the Chinese Clinical Trial Registry (Registration number: ChiCTR2300072179).}, } @article {pmid40593012, year = {2025}, author = {Sitko, K and Piotrowska, E and Podlacha, M and Zagórska, N and Starke, MD and Trzeciak, M and Tukaj, S}, title = {Topical application of the HSP90 inhibitor 17-AAG reduces skin inflammation and partially restores microbial balance: implications for atopic dermatitis therapy.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21245}, pmid = {40593012}, issn = {2045-2322}, support = {2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; }, mesh = {*Benzoquinones/administration & dosage/pharmacology ; *Lactams, Macrocyclic/administration & dosage/pharmacology ; Animals ; *Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism ; *HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism ; Mice ; Humans ; Disease Models, Animal ; Administration, Topical ; *Skin/drug effects/pathology/microbiology ; Female ; Cytokines/metabolism ; Eosinophils/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Staphylococcus aureus/drug effects ; Inflammation/drug therapy ; Keratinocytes/drug effects/metabolism ; }, abstract = {Heat shock proteins belonging to the HSP90 family promote inflammation and are potential therapeutic targets in inflammatory and autoimmune diseases. Here the effects of the HSP90 inhibitor 17-AAG applied topically were evaluated in a DNCB-induced murine model of atopic dermatitis (AD). The use of 17-AAG improved clinical disease activity without causing toxicity in the animals. Topical application of 17-AAG resulted in reduced epidermal hyperplasia, decreased expression of TSLP, IL-5, and IL-6, as well as reduced activation of NF-κB in the skin. In addition, the eosinophil proportion in the blood and eosinophil peroxidase (EPX) activity in the skin were significantly reduced in 17-AAG-treated AD mice. The inhibitory effects of 17-AAG on the production of epidermal alarmins, T-helper cell-associated cytokines, and ROS release were demonstrated in cultures of activated human keratinocytes, CD4[+] T lymphocytes, and eosinophils, respectively. Finally, next-generation sequencing metagenomic approaches revealed that topical application of 17-AAG partially restored the normal gut microbiome in AD mice. Moreover, 17-AAG inhibited Staphylococcus aureus biofilm formation in vitro. The findings of this study, combined with the observed increase in HSP90 and EPX activity in the leukocytes of the analyzed cohort of AD patients, support the potential therapeutic use of HSP90 inhibitors in individuals with AD.}, } @article {pmid40592825, year = {2025}, author = {Mali, N and Mali, S and Zhang, L and Fu, P}, title = {Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.}, journal = {Renal failure}, volume = {47}, number = {1}, pages = {2522976}, pmid = {40592825}, issn = {1525-6049}, mesh = {Humans ; *Acute Kidney Injury/microbiology/immunology/physiopathology ; *Gastrointestinal Microbiome/immunology/physiology ; Kidney/physiopathology/microbiology ; Animals ; }, abstract = {It is unclear, therefore, exactly how gut microbes and renal processes communicate. Recent developments in the field of microbiome research present chances to enhance our comprehension and management of acute kidney injury (AKI). This review highlights important ideas and suggests more research while giving a general summary of the microbiome's influence on kidney function and AKI. AKI is a complex condition that develops through a variety of pathways. Recent experimental research has highlighted the important role that the gut microbiota plays in the course of AKI. Our understanding of human biology has been completely transformed by the current increase in gut microbiota research. Amazing progress in DNA sequencing analysis, especially in the areas of metagenomics and metatranscriptomics, has greatly increased our ability to measure and track complex microbial populations. As such, we are now in a better position to look at how these communities affect human health and illness. As a result, the relationships between renal physiology and pathophysiology and the gut microbiota are now better understood. Both experimental AKI and chronic renal illness have been linked to changes in the intestinal microbiome. This succinct review attempts to examine our present knowledge of the immune-modulatory effects of the gut microbiota, how kidney disorders are influenced by it, and the possible reciprocal interaction between kidney diseases and the microbiota. Subsequent investigations ought to concentrate on delving deeper into the function of the gut microbiota in renal disorders and finding possible therapeutic strategies for adjusting it.}, } @article {pmid40592243, year = {2025}, author = {Gao, Z and Liu, X and Yu, J and Li, Z and Shi, H and Zhang, G and Ling, J}, title = {Structural basis of immunomodulation by edible fungal polysaccharides: From molecular characteristics to action mechanisms.}, journal = {Carbohydrate research}, volume = {555}, number = {}, pages = {109591}, doi = {10.1016/j.carres.2025.109591}, pmid = {40592243}, issn = {1873-426X}, mesh = {Animals ; Humans ; *Fungal Polysaccharides/chemistry/pharmacology ; Gastrointestinal Microbiome/drug effects ; *Immunologic Factors/chemistry/pharmacology ; *Immunomodulating Agents/chemistry/pharmacology ; *Immunomodulation/drug effects ; }, abstract = {Edible Fungal polysaccharides as Immunomodulators: A Systematic Review at the Crossroads of Immunology, Natural Products Chemistry, and Microbiology. The chemical structure-specifically molecular weight, branching degree, and functional group modifications-directly dictates immunological activity. For instance, high-molecular-weight β-glucans activate macrophage surface receptors through triple-helix conformations, whereas sulfation enhances electrostatic interactions with immune cells. Mechanistically, polysaccharides regulate macrophage polarization, dendritic cell maturation, and T/B cell activation, therebyengaging core signaling pathways such as TLR4/MyD88/NF-κB, NLRP3 inflammasome, and MAPK, This orchestrates synergistic enhancement of innate and adaptive immunity. Recent research further demonstrate that polysaccharides can also reshape the gut microbiota-immune metabolic axis by promoting the production of short-chain fatty acids (SCFAs) and activating receptors (e.g., GPR43), indirectly modulating systemic immune responses. Clinically, polysaccharides from Ganoderma lucidum and Lentinus edodes demonstrate efficacy in cancer adjuvant therapy by enhancing immune function and reducing radiotherapy/chemotherapy side effects. However, species-specific receptor recognition heterogeneity and lack of standardized preparation protocols impede clinical translation. Therefore,the implementing an integrated strategy of "polysaccharide structure-immunometabolic reprogramming-precision delivery" to overcome the existing bottlenecks. Combining multi-omics approaches (e.g., gut metagenomics and metabolomics) will advance therapeutics targeting microbiota-immune crosstalk. Such strategies aim to address chronic inflammatory inflammation", malignancies, and related pathologies with enhanced mechanistic specificity.}, } @article {pmid40591379, year = {2025}, author = {Orenburkina, OI and Rezbaeva, GN and Dudurich, VV and Babushkin, AE and Sogomonian, KS and Danilova, AA and Danilov, LG}, title = {[Microbiota of the ocular surface in children with myopia].}, journal = {Vestnik oftalmologii}, volume = {141}, number = {3}, pages = {5-12}, doi = {10.17116/oftalma20251410315}, pmid = {40591379}, issn = {0042-465X}, mesh = {Humans ; Child ; *Myopia/diagnosis/microbiology/physiopathology ; Male ; Female ; Adolescent ; *Microbiota ; *Conjunctiva/microbiology ; *Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; }, abstract = {UNLABELLED: A healthy ocular surface is characterized by relatively stable and comparatively low microbial diversity. However, pathological conditions can provoke shifts in the composition of bacterial taxa, which may be associated, among other factors, with the progression of myopia.

PURPOSE: This study compared the taxonomic diversity of the conjunctival microbiota in children with varying degrees of myopia and those without clinically confirmed myopia.

MATERIAL AND METHODS: Ocular surface samples were obtained from 29 children aged 6-17 years with myopia (58 eyes) and from 12 children of the control group aged 9-17 years (24 eyes). The taxonomic composition of the conjunctival microbiota was analyzed using 16S ribosomal RNA gene (rRNA) sequencing, followed by microbiome profiling through bioinformatics and statistical tools.

RESULTS: The ocular surface microbiota in children with myopia demonstrated higher alpha diversity compared to the control group. This was confirmed by values of the Chao (reflecting low-abundance taxa) and Shannon (reflecting overall bacterial diversity - higher diversity means higher index; optimal value; 3.1-4.2) indices. The results revealed a clear trend toward differentiation in bacterial composition between myopic and control groups. These differences were associated with changes in the relative abundance of opportunistic bacteria depending on the degree of myopia.

CONCLUSION: The taxonomic diversity of the ocular microbiota at the genus level in patients with varying degrees of myopia was characterized by a higher number of taxonomic units compared to the control group. The general trend is an increase in the biodiversity of the bacterial composition due to an increase in the relative representation of opportunistic microorganisms. Further research on the influence of the ocular microbiota on the progression of myopia is needed.}, } @article {pmid40589860, year = {2025}, author = {Nimnoi, P and Pongsilp, N}, title = {Insights into the metagenomic and metabolomic compositions of the bacterial communities in Thai traditional fermented foods as well as the relationships between food nutrition and food microbiomes.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19606}, pmid = {40589860}, issn = {2167-8359}, mesh = {*Fermented Foods/microbiology ; Thailand ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenomics ; Metabolomics ; Fermentation ; }, abstract = {Five Thai traditional fermented foods, including khao-mak (sweet fermented sticky rice), pak-kard-dong (sour salt-fermented mustard greens), nor-mai-dong (sour salt-fermented bamboo sprouts), moo-som (sour salt-fermented pork), and pla-som (sour salt-fermented fish), were analyzed for their food nutrition and bacterial community structures. Sour salt-fermented bamboo sprouts possessed the highest unique amplicon sequence variables (ASVs), which were 3,476, as well as the highest bacterial diversity and richness, while in contrast, sweet fermented sticky rice possessed the lowest such indices. The phylum Firmicutes accounted for the largest proportions in both sour salt-fermented meats and sweet fermented sticky rice whereas the Proteobacteria occupied the largest proportions in both sour salt-fermented vegetables. The bacterial community structures of both sour salt-fermented meats were similar in terms of composition at class level, while the dominant genera compositions were totally different among all foods. Gene functions, enzymes, and metabolic pathways annotated from the bacterial communities in all foods were those involved in growth metabolisms, genetic information processing, environmental information processing, and cellular signaling. Sour salt-fermented bamboo sprouts had the highest numbers of unique annotated genes, enzymes, and metabolic pathways.}, } @article {pmid40586794, year = {2025}, author = {Chadd, EF and Ergunay, K and Kumsa, B and Bourke, BP and Broomfield, BS and Long, LS and Linton, YM}, title = {Nanopore sequencing reveals a diversity of microorganisms in ticks from Ethiopia.}, journal = {Parasitology research}, volume = {124}, number = {7}, pages = {73}, pmid = {40586794}, issn = {1432-1955}, support = {FY23 Award # 23-101//Deployed Warfighter Protection (DWFP) Program/ ; Award # P0031_21_WR//Armed Forces Health Surveillance Division/ ; }, mesh = {Animals ; Ethiopia ; *Nanopore Sequencing ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Ticks/microbiology ; Rickettsia/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; Metagenome ; Phylogeny ; *Biodiversity ; }, abstract = {Ethiopia is home to a diverse group of ixodid ticks that are known to transmit disease to both animals and humans. Recent advances in metagenome sequencing show there is more microorganism diversity found in ticks than previously known. Compared to amplicon-based gene identification methods, agnostic metagenomic sequencing provides broader insights into the diversity of microorganisms in ticks, providing knowledge that will better enable public health measures in preventing the spread of zoonotic disease. In the present study, metagenomic sequencing was used to look at the microbial diversity of ticks collected from livestock in Ethiopia. This study identified six bacterial genera (Coxiella, Francisella, spotted-fever group (SFG) Rickettsia, Spiroplasma, Ehrlichia, and Borrelia), one genus of eukaryotic parasite (Babesia sp.), and one virus species (Parapoxvirus bovinestomatitis) from 154 tick pools representing 22 species of ticks among four genera (Amblyomma, Haemaphysalis, Hyalomma, and Rhipicephalus). We were able to differentiate between pathogenic and nonpathogenic microorganisms, highlighting concerns among traditional gene-targeted screening methods. Among all pooled samples, the predominant microorganisms included Coxiella-like endosymbionts (55.2%), SFG Rickettsia (38.3%), and nonpathogenic Francisella spp. (26.0%). Rickettsia africae was the predominant pathogenic agent detected, and phylogenetic analysis of two samples from A. gemma and A. variegatum confirmed the presence of R. africae. This study highlights the power of metagenomics applied to potential vectors of zoonotic disease, and it expands the knowledge on tick-pathogen associations in Ethiopia.}, } @article {pmid40586597, year = {2025}, author = {Khatib, L and Song, SJ and Dilmore, AH and Sanders, JG and Brennan, C and Hernandez, AR and Myers, T and Oles, R and Farmer, S and Cowart, C and Birmingham, A and Diaz, EA and Nizet, O and Gilbert, K and Litwin, N and Das, P and Nowinski, B and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Chaumont, S and Knol, J and Roeselers, G and Laiola, M and Shetty, SA and Veiga, P and Tap, J and Derrien, M and Koutnikova, H and Cotillard, A and Lay, C and Tovar, AR and Torres, N and Arteaga, L and González, A and McDonald, D and Bartko, A and Knight, R}, title = {A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0054425}, pmid = {40586597}, issn = {2379-5077}, support = {//Danone Nutricia Research/ ; //Center for Microbiome Innovation/ ; //Microsetta Initative/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diet ; Feces/microbiology ; Metagenomics/methods ; Male ; Female ; Adult ; Metagenome ; Prevotella/genetics/classification/isolation & purification ; Middle Aged ; Faecalibacterium/genetics/classification/isolation & purification ; }, abstract = {UNLABELLED: Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.

IMPORTANCE: An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.}, } @article {pmid40586571, year = {2025}, author = {Jiang, Y and An, Z and Li, W and Xia, S and Ding, Q and Zhong, J and Wang, H and Xu, Y and Chen, K and Shen, Y}, title = {Integrated multi-omics reveals the impact of ruminal keystone bacteria and microbial metabolites on average daily gain in Xuzhou cattle.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0076925}, pmid = {40586571}, issn = {2165-0497}, mesh = {Animals ; Cattle/microbiology/growth & development ; *Rumen/microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; China ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; Multiomics ; }, abstract = {UNLABELLED: The rumen microbiome plays a crucial role in determining the metabolic and digestive efficiency of livestock. Despite its crucial role, the impact of the rumen microbiome on average daily gain (ADG) in Xuzhou cattle remains underexplored. Xuzhou cattle is a well-known breed in China, renowned for rapid growth and superior meat quality. We selected 10 individuals from the Xuzhou cattle population and categorized Xuzhou cattle into High-ADG and Low-ADG groups and analyzed their rumen microbiota. Through comprehensive metagenomic and metabolomic analyses, we characterized the microbial diversity and functional composition of the rumen microbiome, uncovering distinct taxonomic and functional alterations associated with ADG. Thirteen kingdoms, 224 phyla, and over 16,000 species were identified, and principal coordinates analysis (PCoA) indicated significant microbial differentiation between the two groups on phylum, genus, and species levels (P < 0.05). Notably, Lentisphaerae, along with several other genera and species, presented a higher abundance in High, suggesting a potential connection with enhanced growth performance. Further functional annotation revealed that the High group displayed enriched carbohydrate and amino acid metabolism pathways, with a greater abundance of carbohydrate-active enzymes (CAZymes), particularly those involved in the degradation of complex carbohydrates. The Low-ADG group exhibited reduced metabolic activity in these pathways. Metabolomic analysis revealed 10 significantly altered metabolites, including gamma-glutamyltyrosine and N-acetylaspartic acid, which were upregulated in the High-ADG group, indicating their potential role in growth promotion. Spearman's rank correlation analysis further uncovered significant interactions between key microbiomes and metabolites, which correlated with ADG. Random forest analysis identified Victivallales and Lentisphaerae as key taxa, with gamma-glutamyltyrosine and Asp-Phe emerging as predictive biomarkers for ADG.

IMPORTANCE: This study identifies key microbiota (Victivallales and Lentisphaerae) and metabolites (gamma-glutamyltyrosine, Asp-Phe, N-acetylaspartic acid, Gly-Phe) that positively regulate average daily gain (ADG) in Xuzhou cattle through amino acid metabolism. This fundamental information is vital for the development of potential manipulation strategies to improve the daily gain level through precision feeding.}, } @article {pmid40586543, year = {2025}, author = {Begmatov, S and Beletsky, AV and Mardanov, AV and Lukina, AP and Glukhova, LB and Karnachuk, OV and Ravin, NV}, title = {Novel lineages of bacteria with reduced genomes from the gut of farm animals.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0029425}, pmid = {40586543}, issn = {2379-5042}, support = {//Ministry of Science and Higher Education of the Russian Federation (Minobrnauki of Russia)/ ; }, mesh = {Animals ; *Genome, Bacterial ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Phylogeny ; *Animals, Domestic/microbiology ; Metagenomics ; Cattle ; Sheep ; Horses/microbiology ; }, abstract = {Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.}, } @article {pmid40586542, year = {2025}, author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER}, title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.}, journal = {mSphere}, volume = {10}, number = {7}, pages = {e0025725}, pmid = {40586542}, issn = {2379-5042}, mesh = {Humans ; *Dental Caries/microbiology/etiology ; *Biofilms/growth & development ; *Head and Neck Neoplasms/radiotherapy/complications ; Male ; Female ; *Microbiota ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Radiotherapy/adverse effects ; }, abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.

IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.}, } @article {pmid40586419, year = {2025}, author = {Dason, MS and Corà, D and Re, A}, title = {Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0033325}, pmid = {40586419}, issn = {2379-5077}, support = {P2022AFS8P//Next Generation EU - MUR/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Biosynthetic Pathways/genetics ; Multigene Family ; *Computational Biology/methods ; Bacteria/genetics/metabolism ; }, abstract = {Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.}, } @article {pmid40585302, year = {2025}, author = {Louca, S}, title = {Machine learning models for delineating marine microbial taxa.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf090}, pmid = {40585302}, issn = {2631-9268}, mesh = {*Machine Learning ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Metagenome ; Phylogeny ; Genome, Bacterial ; *Aquatic Organisms/genetics/classification ; }, abstract = {The relationship between gene content differences and microbial taxonomic divergence remains poorly understood, and algorithms for delineating novel microbial taxa above genus level based on multiple genome similarity metrics are lacking. Addressing these gaps is important for macroevolutionary theory, biodiversity assessments, and discovery of novel taxa in metagenomes. Here, I develop machine learning classifier models, based on multiple genome similarity metrics, to determine whether any two marine bacterial and archaeal (prokaryotic) metagenome-assembled genomes (MAGs) belong to the same taxon, from the genus up to the phylum levels. Metrics include average amino acid and nucleotide identities, and fractions of shared genes within various categories, applied to 14 390 previously published non-redundant MAGs. At all taxonomic levels, the balanced accuracy (average of the true-positive and true-negative rate) of classifiers exceeded 92%, suggesting that simple genome similarity metrics serve as good taxon differentiators. Predictor selection and sensitivity analyses revealed gene categories, e.g. those involved in metabolism of cofactors and vitamins, particularly correlated to taxon divergence. Predicted taxon delineations were further used to de novo enumerate marine prokaryotic taxa. Statistical analyses of those enumerations suggest that over half of extant marine prokaryotic phyla, classes, and orders have already been recovered by genome-resolved metagenomic surveys.}, } @article {pmid40582607, year = {2025}, author = {Páez-Triana, L and Luna, N and Cruz-Saavedra, L and Ramírez, AL and Medina, JE and Castañeda, S and Gómez, M and Garcia-Corredor, DJ and Medellín, MOP and Patiño, LH and Muñoz, M and Ramirez, JD}, title = {Characterizing the diversity of Rhipicephalus sanguineus sensu lato (s.l) virome in Colombia.}, journal = {Acta tropica}, volume = {268}, number = {}, pages = {107715}, doi = {10.1016/j.actatropica.2025.107715}, pmid = {40582607}, issn = {1873-6254}, mesh = {Animals ; Colombia ; *Rhipicephalus sanguineus/virology ; *Virome ; Phylogeny ; Dogs ; Genome, Viral ; *RNA Viruses/genetics/classification/isolation & purification ; Nanopore Sequencing ; Female ; }, abstract = {Ticks within the species complex Rhipicephalus sanguineus sensu lato are carriers for various pathogens worldwide. Among them are some RNA viruses, who have gained increased attention due to their potential for interaction between pathogenic and non-pathogenic organism. Our study aimed to investigate the RNA virus composition in R. sanguineus s.l. (also known as R. linnaei) ticks collected from the Santander and Casanare regions in eastern Colombia. We employed Oxford Nanopore sequencing technology coupled with viral enrichment procedures. Thirty-nine adult ticks, removed from dogs, were sequenced with Oxford Nanopore sequencing. These reads underwent two distinct analyses: one focused on sequencing reads utilizing Centrifuge/BLAST for direct assignment, and one involved assembly of viral metagenomic assembled genomes (vMAGs) using the Genome Detective Tool program. Our investigation showed the presence of six distinct viruses within the tick virome: Trinbago virus, Mivirus sp., Bole tick virus 4, Brown dog tick phlebovirus 2, Totiviridae sp., Ixodes scapularis totilike virus, and Brown dog tick phlebovirus 1. Notably, we successfully assembled the genomes for the latter two species, enabling phylogenetic and comparative analyses with genomes from various global regions. Only the category of sex yield significant differences in alpha diversity. We described viruses with potential pathogenicity but also with endosymbiotic potential. The latter group holds promise for developing biotechnological tools to aid future tick vector control strategies. Furthermore, our research offered valuable insights into the predominant viruses found in R. sanguineus s.l. ticks in two previously unexplored regions within Colombia.}, } @article {pmid40582136, year = {2025}, author = {Song, L and Hu, C and Zhang, X and Liu, Y and Song, G and Wu, J and Wang, Z and Sun, M}, title = {Effects of feeding on microbial community structure and pathogen abundance in marine aquaculture ponds.}, journal = {Marine environmental research}, volume = {210}, number = {}, pages = {107319}, doi = {10.1016/j.marenvres.2025.107319}, pmid = {40582136}, issn = {1879-0291}, mesh = {*Aquaculture ; *Ponds/microbiology ; *Microbiota ; Eutrophication ; Bacteria ; *Water Microbiology ; Water Quality ; Animals ; }, abstract = {Microbial communities in aquaculture ponds play a vital role in regulating water quality, driving nutrient cycling, and maintaining ecological balance. In 2023, we conducted a study to evaluate how feeding affects microbial communities by comparing the microbial composition and water quality in both fed and unfed aquaculture ponds. Metagenomic sequencing indicated that feeding significantly elevated the relative abundance of bacteria within the microbial community. Ecological similarity analysis showed that bacterial community in the ponds predominantly originated from internal pond sources, rather than from adjacent coastal waters. Furthermore, the relative abundance of pathogenic bacteria was significantly higher in fed ponds, with Vibrio parahaemolyticus levels reaching 1.6 times those in unfed ponds. In addition, water quality assessments further showed that feeding elevated nutrient concentrations, leading to eutrophication. Analyses of redundancy and correlation showed a notable positive link (p < 0.05) between the levels of pathogenic bacteria and the concentration of organic nutrients. These results suggest that excessive feeding contributes to eutrophication, which promotes the growth of bacteria, including pathogenic strains, thereby increasing the risk of disease outbreaks in aquaculture systems.}, } @article {pmid40580323, year = {2025}, author = {Callejas, C and Guerrero, L and Erijman, L and López, I and Borzacconi, L}, title = {Microbiota and methanogenic activities in an anaerobic internal circulation reactor: insights into biogas production from brewery wastewater.}, journal = {Biodegradation}, volume = {36}, number = {4}, pages = {56}, pmid = {40580323}, issn = {1572-9729}, support = {2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; }, mesh = {*Bioreactors/microbiology ; *Methane/metabolism ; *Microbiota ; *Biofuels/microbiology ; *Wastewater/microbiology ; Anaerobiosis ; Archaea/metabolism/genetics/classification ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; }, abstract = {In this study, we analyzed the prokaryotic community and methanogenic activities in sludge samples collected from a full-scale internal circulation (IC) reactor used to treat brewery wastewater. The reactor performance was monitored over 15 months, and specific methanogenic activities were periodically measured in fresh sludge samples using CO2/H2 or acetate as substrates. The maximum hydrogenotrophic activities were consistently higher than maximum acetoclastic activities, suggesting the relevance of hydrogenotrophic methanogens in the sludge. Over six months, the prokaryotic community present in four sludge samples was analyzed using amplicon libraries and metagenomics. V4-16S rRNA amplicon libraries revealed the presence of a diverse microbial community dominated by Firmicutes and Bacteroidetes among bacterial phyla, and Halobacterota and Euryarchaeota among archaea. Furthermore, the 16S libraries constructed with cDNA were consistent with the methanogenic activity assays. A genome-centric metagenomics approach was used to assemble 42 high-quality metagenome-assembled genomes (MAGs), among which Methanothrix and Methanobacterium were the dominant archaeal members, and Acidobacteriota, Synergistota, Krumholzibacteriota, and Nitrospirota phyla were among the bacteria. Potential acetogenic members were explored via the fths gene; 15 MAGs contained this marker gene. A combination of methanogenic activity tests, amplicon libraries, and MAG analysis was used to gain insights into the prokaryotic structure and functional potential of the microbial community driving methane production in the reactor.}, } @article {pmid40580234, year = {2025}, author = {Biessy, L and Sissons, J and Kihika, JK and Wood, SA and Pearman, JK}, title = {Microbial adaptations to acidic, nutrient- and metal-rich lakes in Aotearoa New Zealand.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {2}, pages = {24}, pmid = {40580234}, issn = {1433-4909}, mesh = {*Lakes/microbiology/chemistry ; New Zealand ; *Microbiota ; *Adaptation, Physiological ; Geologic Sediments/microbiology ; *Metals/analysis ; Nutrients/analysis ; Bacteria/genetics/metabolism ; }, abstract = {Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.}, } @article {pmid40578342, year = {2025}, author = {Wong, KK and Wu, BG and Chung, M and Li, Q and Darawshy, F and Tsay, JJ and Holub, M and Barnett, CR and Kwok, B and Kugler, MC and Chung, C and Natalini, JG and Singh, S and Li, Y and Schluger, R and Ficaro, L and Carpenito, J and Collazo, D and Perez, L and Kyeremateng, Y and Chang, M and Czachor, A and Singh, R and Mccormick, C and Campbell, CD and Keane, R and Askenazi, M and Hansbro, PM and Weiden, MD and Huang, YJ and Stringer, KA and Clemente, JC and Li, H and Jones, D and Ghedin, E and Segal, LN and Sulaiman, I}, title = {Microbial contribution to metabolic niche formation varies across the respiratory tract.}, journal = {Cell host & microbe}, volume = {33}, number = {7}, pages = {1073-1088.e6}, doi = {10.1016/j.chom.2025.06.002}, pmid = {40578342}, issn = {1934-6069}, support = {R35 GM136312/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; Humans ; *Microbiota ; Metabolome ; *Respiratory System/microbiology/metabolism ; Lung/microbiology/metabolism ; Prevotella/metabolism ; Female ; Mice, Inbred C57BL ; Male ; Methionine/metabolism ; Metagenome ; Streptococcus/metabolism ; *Bacteria/metabolism/classification/genetics ; Veillonella/metabolism ; Glutamic Acid/metabolism ; }, abstract = {Variations in the airway microbiome are associated with inflammatory responses in the lung and pulmonary disease outcomes. Regional changes in microbiome composition could have spatial effects on the metabolic environment, contributing to differences in the host response. Here, we profiled the respiratory microbiome (metagenome/metatranscriptome) and metabolome of a patient cohort, uncovering topographical differences in microbial function, which were further delineated using isotope probing in mice. In humans, the functional activity of taxa varied across the respiratory tract and correlated with immunomodulatory metabolites such as glutamic acid/glutamate and methionine. Common oral commensals, such as Prevotella, Streptococcus, and Veillonella, were more functionally active in the lower airways. Inoculating mice with these commensals led to regional increases in several metabolites, notably methionine and tyrosine. Isotope labeling validated the contribution of Prevotella melaninogenica in generating specific metabolites. This functional characterization of microbial communities reveals topographical changes in the lung metabolome and potential impacts on host responses.}, } @article {pmid40578039, year = {2025}, author = {Wen, Y and Li, M and Hao, Y and Peng, J and Wei, X and Zhang, Z and Liu, B and Wang, Y and Peng, T and Ma, Y}, title = {HDAC/NF-κB signaling pathway mediates gut microbiota dysbiosis in rheumatoid arthritis: Intervention mechanisms of Fengshining decoction.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {156976}, doi = {10.1016/j.phymed.2025.156976}, pmid = {40578039}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Arthritis, Rheumatoid/drug therapy/microbiology/metabolism ; *Dysbiosis/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology ; *NF-kappa B/metabolism ; Mice ; *Arthritis, Experimental/drug therapy/microbiology ; Signal Transduction/drug effects ; Male ; *Histone Deacetylases/metabolism ; Fecal Microbiota Transplantation ; Butyrates/pharmacology ; Fatty Acids, Volatile/metabolism ; Mice, Inbred DBA ; }, abstract = {BACKGROUND: Gut microbiota dysbiosis has been associated with the development of rheumatoid arthritis (RA). Fengshining (FSN) is a traditional Chinese medicine decoction that can effectively alleviate RA. However, how FSN modulates the gut microbiota to mitigate RA has not been comprehensively studied. This study evaluated the gut microecological mechanisms underlying FSN's effects on RA, focusing on the impact of gut-derived short-chain fatty acids (SCFAs), specifically butyrate, in RA treatment.

METHODS: The pharmacological effects of FSN on type II collagen-induced arthritis (CIA) in mice were assessed via pathological indicators, metagenomics, and metabolomics analyses. Furthermore, the impact of FSN on gut microbiota and metabolic profiles was also evaluated. Moreover, a pseudo-germ-free CIA model was established to validate whether exogenous butyrate alleviates RA. This study also elucidated whether fecal microbiota transplantation (FMT) from FSN-treated mice could mitigate RA symptoms.

RESULTS: The data showed that FSN markedly alleviated CIA symptoms and reduced serum inflammatory cytokine levels. Metagenomic and metabolomic analyses revealed that FSN-enriched SCFA-producing bacteria, including Butyrivibrio, Faecalicatena, and Lacrimispora. Furthermore, FSN increased the activity of carbohydrate metabolism-related enzymes and upregulated the expression patterns of homologous protein families. Moreover, exogenous butyrate supplementation suppressed pro-inflammatory factors, modulating immune responses, and enhanced intestinal barrier function. Further, Western blot analysis validated that FSN inhibited the HDAC/NF-κB pathway.

CONCLUSION: This study indicated that the gut microecological mechanism of FSN might be associated with its herbal components, which regulate gut microbiota diversity, restore the intestinal barrier, and boost microbial metabolite production. Furthermore, butyrate was observed to modulate intestinal mucosa, inhibit inflammatory responses, repair the intestinal barrier, and mitigate joint damage, thus alleviating RA symptoms.}, } @article {pmid40575481, year = {2025}, author = {Chen, L and Li, Z and Yuan, D and Chen, Y and Xu, Y and Tang, W and Liu, C}, title = {Microorganism changes in the gut of Apis mellifera surviving for the long term in Camellia oleifera forests.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1608835}, pmid = {40575481}, issn = {2235-2988}, mesh = {Animals ; Bees/microbiology ; *Camellia ; *Gastrointestinal Microbiome ; Oligosaccharides/metabolism ; Forests ; Metabolomics ; Metagenomics ; *Gastrointestinal Tract/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; }, abstract = {Alpha-galactosides (oligosaccharides) in C. oleifera nectar and pollen cause honey bee larval rot and worker bloats. Honey bee colonies surviving in C. oleifera forests for a long period have low rates of larval rot and worker bloats; however, the mechanism of oligosaccharide metabolism is unclear. In this study, we used metagenomics and metabolomics to investigate the structure and function of the gut flora and the digestion characteristics of oligosaccharides in the gut of A. mellifera foragers (CN group) that had been in the C. oleifera forest for a long period (continuously for 14 years), and those that had not been pollinated with C. oleifera (N group) after 24 h of consumption of C. oleifera honey. The results revealed that the abundance of Gilliamella apicola up to 24.08%, which can metabolize α-galactoside (α-Gal), was significantly higher (P < 0.05) in the gut of foragers in the CN group than in the N group. Additionally, the gut flora of foragers in the CN group carried a significantly higher (P < 0.05) abundance of genes encoding α-galactosidase (Glycoside hydrolase family 4, GH4) than the N group. Similarly, metabolomic results indicated that the three toxic oligosaccharides in C. oleifera honey were lower in the gut of CN group foragers. These results suggest that the gut flora of A. mellifera, which inhabits oil tea forests for long periods of time, changes and adapts to the predominant ecological niche, enhancing the host's ability to metabolize toxic oligosaccharides. This important discovery provides positive guidance for the subsequent directions for breeding of A. mellifera (G. apicola enrichment and GH4 upregulation), specialized in pollinating C. oleifera.}, } @article {pmid40573768, year = {2025}, author = {Giménez-Valero, C and Maciá-Vázquez, AA and Núñez-Gómez, D and Conesa, A and Lidón, V and Melgarejo, P}, title = {Evolution of the Soil Bacterial Community as a Function of Crop Management: A Metagenomic Study in Orange Tree (Citrus sinensis) Plantations.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {40573768}, issn = {2223-7747}, support = {AGROALNEXT program (AGROALNEXT 2022/013, SIRIS Project)//European Union/ ; }, abstract = {Soil management significantly influences the structure and diversity of soil bacterial communities, affecting biodiversity and ecosystem functions. In semi-arid regions, water efficiency strategies like anti-weed netting are implemented, but their impact on soil microbial communities remains underexplored. This study evaluates the temporal evolution of soil bacterial communities in orange tree (Citrus sinensis (L.) Osbeck) plantations under two conditions: with and without anti-weed netting. Soil samples were collected at three time points over a period of 18 months since the establishment of the crop and analyzed using high-throughput 16S rRNA sequencing, assessing alpha and beta diversity, taxonomic composition, and functional pathways via KEGG analysis. The results indicate that weed control netting contributes to stabilizing bacterial diversity over time and increases the relative abundance of dominant phyla such as Planctomycetota, Proteobacteria, Bacteroidota, and Acidobacteriota. Functional predictions revealed significant differences in metabolic pathways, including those associated with nitrogen fixation and organic matter degradation. These findings suggest that anti-weed netting not only influences the taxonomic composition of soil bacterial communities but also modulates their functional potential, with implications for sustainable agriculture in semi-arid environments. This study provides new insights into the interaction between soil management and soil bacterial communities, offering valuable information for optimizing agricultural practices and soil conservation strategies.}, } @article {pmid40573403, year = {2025}, author = {Zhang, X and Fan, IX and Xu, Y and Rule, J and Tse, LPV and Pourkarim, MR and Lee, WM and Di Bisceglie, AM and Fan, X}, title = {Novel Viral Sequences in a Patient with Cryptogenic Liver Cirrhosis Revealed by Serum Virome Sequencing.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, pmid = {40573403}, issn = {1999-4915}, support = {1R21AI175438-24/NH/NIH HHS/United States ; R21 AI175438/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Liver Cirrhosis/virology ; *Virome/genetics ; Male ; Middle Aged ; Female ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Metagenomics ; Aged ; Sequence Analysis, DNA ; Adult ; *Serum/virology ; }, abstract = {Clinical studies indicate the etiology of liver disease to be unknown in 5% to 30% of patients. A long-standing hypothesis is the existence of unknown viruses beyond hepatitis A through E virus. We conducted serum virome sequencing in nine patients with cryptogenic liver disease and identified eight contigs that could not be annotated. One was determined to be a contaminant, while two of seven contigs from an individual (Patient 3) were validated by reverse transcription and polymerase chain reaction (RT-PCR) and Sanger sequencing. The possibility of contamination was completely excluded through PCR, with templates extracted using different methods from samples taken at different time points. One of the contigs, Seq260, was characterized as negative-sense single-stranded DNA via enzymatic digestion and genome walking. Digital-droplet PCR revealed the copy number of Seq260 to be low: 343 copies/mL. Seq260-based nested PCR screening was negative in 200 blood donors and 225 patients with liver disease with/without known etiologies. None of the seven contigs from Patient 3 was mapped onto 118,713 viral metagenomic data. Conclusively, we discovered seven unknown contigs from a patient with cryptogenic liver cirrhosis. These sequences are likely from a novel human virus with a negative-sense, linear single-stranded DNA genome.}, } @article {pmid40573349, year = {2025}, author = {Hernández-Villegas, EN and Castelán-Sánchez, HG and Moreira-Soto, A and Vigueras-Galván, AL and Jiménez-Rico, MA and Rico-Chávez, O and Rodríguez-González, S and Tolsá-García, MJ and Roiz, D and Martínez-Duque, P and Arana-Guardía, R and García-Súarez, O and Jiménez, MZ and Falcón, LI and Roche, B and Sarmiento-Silva, RE and Arnal, A and Drexler, JF and Suzán, G}, title = {Characterization of the Virome in Mosquitoes Across Distinct Habitats in the Yucatán Peninsula, Mexico.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, pmid = {40573349}, issn = {1999-4915}, mesh = {Animals ; Mexico ; *Culicidae/virology ; *Ecosystem ; *Virome ; *Mosquito Vectors/virology ; *Viruses/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Genome, Viral ; Biodiversity ; }, abstract = {Human activities and land use changes have a major impact on the distribution and diversity of mosquito vectors and their associated viruses. This study describes the diversity and differential abundance of viruses associated with mosquito species from four habitats of the Yucatan Peninsula, Mexico. Using next-generation sequencing (NGS), we analyzed 61 genomic libraries belonging to 20 mosquito species to characterize the viral community. A total of 16 viral species were identified, representing 14 different viral families. Most identified viruses were associated with insects, plants, and fungi. Additionally, vertebrate associated viral families, including Herpesviridae, Peribunyaviridae, Nairoviridae, and Arenaviridae, were detected in mosquitoes from urban habitats. Notably, insect-associated viruses like Hubei mosquito virus 4 and Hubei virga-like virus 2 were identified, along with the first report of Mercadeo virus in Mexico. Variations in viral community composition were primarily driven by mosquito species, with species of the same genus maintaining similar viromes despite occupying different habitats. These findings reinforce that intrinsic traits of mosquito species play a key role in shaping viral community composition. To our knowledge, this is the first study that describes the viral community in mosquitoes in Yucatan Peninsula, Mexico. This study provides essential baseline data for the surveillance of mosquitoes and associated viruses from a biodiverse tropical region that faces strong land use modifications.}, } @article {pmid40572043, year = {2025}, author = {Yang, C and Sun, J and Li, L and Zheng, J and Wang, C and Zhao, Y and Yun, D and Jia, M and Wu, Z and Liang, H and Li, W and Hu, T and Guo, R and Xiao, L and Zou, Y and Liu, Z}, title = {Synbiotics of Lactobacillus suilingensis and inulin alleviates cognitive impairment via regulating gut microbiota indole-3-lactic acid metabolism in female AD mice.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {7}, pages = {e70406}, pmid = {40572043}, issn = {1552-5279}, support = {2022ZD0208100//National Science and Technology Innovation 2030-Major Program of Brain Science and Brain-Like Research/ ; 32241012//National Natural Science Foundation of China/ ; 32472351//National Natural Science Foundation of China/ ; JCYJ20220818102810022//Shenzhen Science and Technology Program/ ; XMHT20220104017//Shenzhen Municipal Government of China/ ; 2022A1515110717//Regional Consolidated Fund-Youth Fund Project in Guangdong Province/ ; BGIRSZ20220009//open project of BGI-shenzhen/ ; //China Biotechnology Development Center/ ; //Shenzhen Science and Technology Innovation Commission/ ; //Shenzhen Municipal Government/ ; //Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Inulin/pharmacology/administration & dosage ; Female ; *Cognitive Dysfunction/metabolism ; Mice ; *Synbiotics/administration & dosage ; *Indoles/metabolism ; *Alzheimer Disease/metabolism ; Humans ; Tryptophan/metabolism ; Disease Models, Animal ; Receptors, Aryl Hydrocarbon/metabolism ; Probiotics ; }, abstract = {INTRODUCTION: Recent studies have found that gut microbial tryptophan metabolism is altered in Alzheimer's disease (AD) patients. However, the functional consequences of these changes and their therapeutic potential remain unclear.

METHODS: The metagenomic data of 49 preclinical AD patients and 115 healthy controls were analyzed. A synbiotic with targeted metabolic functions was formulated based on in vitro testing, and its effect on AD was evaluated using female 5×FAD mice.

RESULTS: Indole lactic acid (ILA) synthesis was downregulated in AD patients. Synbiotic treatment combining Lactobacillus suilingensis and inulin outperformed probiotic treatment alone in enhancing tryptophan metabolism, and increasing ILA biosynthesis. Increased ILA could reduce Aβ accumulation and significantly alleviate cognitive impairment in female AD mice by inhibiting neuroinflammation through activation of the aryl hydrocarbon receptor (AhR) signaling pathway.

DISCUSSION: This study highlights the therapeutic potential of targeting gut microbial tryptophan metabolism in AD and provides a rationale for future precision strategies aimed at modulating microbiota-derived metabolic pathways.

HIGHLIGHTS: Gut metagenomic analysis reveals reduced indole lactic acid (ILA) biosynthesis genes in preclinical AD patients. Screening and formulating ILA-producing synbiotic by using whole-genome analysis. Synbiotic treatment alleviates cognitive impairment and promotes ILA synthesis in female 5×FAD mice. ILA alleviates neuroinflammation in female 5×FAD mice by activating aryl hydrocarbon receptor (AhR) in the brain. Synbiotic targeting tryptophan metabolism provides a novel approach for Alzheimer's intervention.}, } @article {pmid40571109, year = {2025}, author = {Chen, H and Qiu, X and Lei, S and Zhao, Y and Zhang, M and Gao, M and Guo, R and Di, H and Huang, J and Yu, Z}, title = {Gut vs. vaginal microbiome in diabetes Progression: Key microbial shifts and implications.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107833}, doi = {10.1016/j.micpath.2025.107833}, pmid = {40571109}, issn = {1096-1208}, mesh = {Humans ; Female ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; *Vagina/microbiology ; Middle Aged ; Feces/microbiology ; Disease Progression ; Metagenomics ; Aged ; Blood Glucose/analysis ; Glycated Hemoglobin/analysis ; Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Dysbiosis/microbiology ; Adult ; }, abstract = {BACKGROUND: Dysiosis in gut and vaginal microbiome is implicated in type 2 diabetes (T2D) pathogenesis, but their contributions remain unclear. This study aims to compare their alterations and clinical relevance in diabetes development.

METHODS: Metagenomic sequencing was performed on vaginal and fecal samples from T2D patients. Differential feature selection and correlation model were used to dissect microbial contributions to diabetic markers.

RESULTS: Gut microbiota exhibited reduced diversity in T2D patients, with enrichment of Desulfovibrio desulfuricans and Adlercreutzia equolifaciens validated in public cohorts. Vaginal microbiota diversity remained unaffected. Furthermore, structural equation modeling revealed stronger gut microbiota associations with blood glucose and HbA1c. Notably, Romboutsia ilealis-derived pgm was enriched in the diabetes group, which could catalyze the production of glucose, suggesting that it may be involved in the progression of T2D.

CONCLUSION: Our findings establish the gut microbiome as the dominant driver of T2D progression, with R. ilealis emerging as a potential therapeutic target. This highlights the priority of gut-centric microbiota interventions in diabetes management.}, } @article {pmid40571107, year = {2025}, author = {Chen, J and Chen, Z and Xu, B and Huang, Z and Zhang, C}, title = {Skin microbiome of Asian elephants with skin diseases during seasonal transitions.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107832}, doi = {10.1016/j.micpath.2025.107832}, pmid = {40571107}, issn = {1096-1208}, mesh = {Animals ; *Skin/microbiology ; *Microbiota/genetics ; *Elephants/microbiology ; Seasons ; Virulence Factors/genetics ; *Skin Diseases/microbiology/veterinary ; Metagenomics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Staphylococcus/genetics/isolation & purification ; Computational Biology ; Sequence Analysis, DNA ; Skin Microbiome ; }, abstract = {INTRODUCTION: Wild Asian elephants (Elephas maximus), which are an endangered species, often suffer from skin diseases during seasonal transitions, which seriously affect their health. Understanding the pathogenesis of such skin diseases is critical for their prevention and treatment. It is known that skin microorganisms are closely related to host skin health.

OBJECTIVE: To compare the microbiotas and microbiomes of diseased and healthy skin of Asian elephants.

METHODS: DNA was extracted from skin swab samples from diseased and healthy Asian elephants for metagenomic sequencing. Various bioinformatic tools were used to process the raw sequencing data and identify gene sequences for functional annotation and species identification as well as to determine species abundance. Antibiotic resistance genes and virulence factors were also identified using DIAMOND.

RESULTS: Staphylococcus was highly enriched in the microbiota of diseased skin, whereas Leuconostoc predominated in that of healthy skin. Moreover, substantial differences existed between the two elephant skin groups in terms of metabolic pathways related to ATP-binding cassette transporters and TCSs and the abundance of antibiotic resistance genes and Staphylococcus-associated toxins. The substantial difference in Staphylococcus-related virulence factors was likely due to the significant enrichment of Staphylococcus in the diseased skin samples, suggesting that this bacterial genus is the causative agent of skin diseases in Asian elephants. Additionally, Leuconostoc mesenteroides, which was enriched in the healthy skin samples, has anti-inflammatory, antimicrobial, and other beneficial effects that have promising applications in the prevention, diagnosis, and treatment of skin diseases.

CONCLUSION: This study reveals the cause of skin diseases in Asian elephants and provides a theoretical basis for improving the skin health of wild animals and expanding wildlife conservation methods and technologies.}, } @article {pmid40570762, year = {2025}, author = {Pateriya, D and Malwe, AS and Sharma, VK}, title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.}, journal = {Computers in biology and medicine}, volume = {195}, number = {}, pages = {110592}, doi = {10.1016/j.compbiomed.2025.110592}, pmid = {40570762}, issn = {1879-0534}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Machine Learning ; Deep Learning ; Algorithms ; }, abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.}, } @article {pmid40570415, year = {2025}, author = {Yin, Z and Cao, K and Duan, N and Zhang, Z}, title = {Microbial community dynamics and functional potential during the natural fermentation of rose: A metagenomic and volatile compound analysis.}, journal = {Enzyme and microbial technology}, volume = {190}, number = {}, pages = {110703}, doi = {10.1016/j.enzmictec.2025.110703}, pmid = {40570415}, issn = {1879-0909}, mesh = {Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenome ; *Microbial Consortia/genetics ; Butylene Glycols/metabolism ; }, abstract = {This study investigates the dynamics of microbial communities and their functional characteristics during the natural fermentation of roses. Utilizing metagenomic sequencing and volatile compound analysis, the research elucidates the succession of microbial communities and their relationship with the flavor compound production. The findings indicate that Klebsiella and Pichia are predominant in the early stages of fermentation, while Acetobacter and Cyberlindnera become more abundant in the middle and later stages. The glycosyltransferase (GT) family is identified as the primary carbohydrate-active enzyme (CAZy) family involved in fermentation, with GT1 and GT2 exhibiting a higher gene abundance. Functional genes are predominantly associated with the carbohydrate and amino acid metabolism. Analysis of volatile compounds reveals that substances such as phenethyl acetate and (S,S)-2,3-Butanediol are closely related to the structure of the microbial community. These findings contribute to a deeper understanding of the mechanisms underlying rose fermentation and offer a theoretical foundation for technological advancements in the rose product industry.}, } @article {pmid40570246, year = {2025}, author = {Ma, C and Bao, Y and Hereid, S and Zhang, H and Bai, X and Bai, Q and Zhao, L and Zhang, X and Lian, H and Dai, L and Bao, X and Bao, L}, title = {Mechanistic Elucidation of Tricholoma mongolicum Polysaccharides in Treating MAFLD via Regulation of the Gut Microbiota-Metabolite-Ferroptosis Axis: A Multi-Omics Perspective.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {27}, pages = {17040-17056}, pmid = {40570246}, issn = {1520-5118}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/administration & dosage/chemistry ; Animals ; Mice ; Male ; Humans ; *Tricholoma/chemistry ; Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Iron/metabolism ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/genetics ; *Plant Extracts/administration & dosage/chemistry ; *Fatty Liver/drug therapy/metabolism/microbiology/genetics ; Multiomics ; }, abstract = {This study aimed to elucidate the modulatory effects and underlying molecular mechanisms of Tricholoma mongolicum polysaccharide (TMP) in the context of metabolic dysfunction-associated fatty liver disease (MAFLD). High-performance gel permeation chromatography (HPGPC) analysis indicated a bimodal molecular weight distribution. Monosaccharide composition profiling revealed a predominance of glucose and galactose among other constituents. Scanning electron microscopy (SEM) illustrated a porous, aggregated colloidal microstructure. In a model of MAFLD, TMP intervention significantly attenuated serum levels of TC, TG, and AST, ALT, accompanied by notable histological improvements, including reduced hepatic steatosis and inflammatory cell infiltration. Metagenomic analysis demonstrated that TMP substantially enhanced gut microbial α-diversity, restructured microbial community composition, decreased the Firmicutes/Bacteroidetes ratio, enriched SCFAs-producing genera, and suppressed the excessive proliferation of pro-inflammatory bacterial genera. Integrated proteomic and lipidomic analyses revealed that TMP inhibited hepatic immune-inflammatory responses and ferroptosis pathways, enhanced pathways associated with metabolic homeostasis. Furthermore, TMP modulated hepatic iron metabolism by upregulating the Nrf2/GPx4 antioxidant axis and FPN1 while downregulating TFR1, thereby alleviating oxidative stress and iron overload. These findings demonstrate that TMP exerts therapeutic efficacy through a bidirectional gut-liver regulatory mechanism involving microbial modulation, ferroptosis inhibition, metabolic reprogramming, and activation of antioxidant defenses. This research provides novel insights and molecular targets for the development of natural polysaccharide-based interventions for MAFLD.}, } @article {pmid40570071, year = {2025}, author = {Savelieva, EI and Shachneva, MD}, title = {Problems and prospects of metabolomic studies in the alteration of the gut microbiome.}, journal = {Biomeditsinskaia khimiia}, volume = {71}, number = {3}, pages = {195-208}, doi = {10.18097/PBMCR1556}, pmid = {40570071}, issn = {2310-6972}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metabolome ; Animals ; Bile Acids and Salts/metabolism ; *Renal Insufficiency, Chronic/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {The review summarizes existing knowledge on the relationship between certain diseases and alteration (degeneration) of the intestinal microbiome. We consider major microbial metabolites firmly recognized as signaling molecules acting in communication between the microbiome and the host organism. These include short-chain fatty acids, bile acids, amines, amino acids, and their metabolites. Special attention is paid to metabolomic studies of the microbiome in chronic kidney diseases, in particular, immunoglobulin A nephropathy. The arguments supporting a concept of the microbiome of blood, previously considered an exclusively sterile environment in healthy humans, are considered. Metagenomic methods plays a key role in characterization of both the composition and potential physiological effects of microbial communities. The advantages and limitations of metabolomic analysis of blood serum/plasma and feces have been analyzed. Since the potential of clinical studies of the mutual impact of the microbiome-metabolome is limited by genetic and external factors, preclinical studies still employ both germ-free models and models based on the effects of antibiotics. The review considers the problems and prospects of metabolomics in studying the nature and mechanisms of the mutual impact of the microbiome and metabolome.}, } @article {pmid40569902, year = {2025}, author = {Belheouane, M and Kalsdorf, B and Niemann, S and Gaede, KI and Lange, C and Heyckendorf, J and Merker, M}, title = {Serratia sp. traits distinguish the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325362}, pmid = {40569902}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; Male ; Middle Aged ; *Lung/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; Adult ; *Serratia/genetics/isolation & purification/classification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/genetics ; *Tuberculosis, Pulmonary/microbiology ; *Lung Diseases/microbiology ; }, abstract = {BACKGROUND: Pathogenic mycobacteria, such as Mycobacterium tuberculosis complex (Mtbc), and non-tuberculous mycobacteria (NTMs) can cause severe chronic pulmonary infections. However, not all infected patients develop active disease, and it remains unclear whether key lung microbiome taxa play a role in the pathogenesis of tuberculosis (TB) and NTM lung diseases (LD). Here, we aim to further define the lung microbiome composition in TB, and NTM-LD prior to the initiation of therapy.

STUDY DESIGN: We employed 16S rRNA amplicon sequencing to characterize the baseline microbiome in bronchoalveolar lavage fluid (BALF) from patients diagnosed with TB (n = 23), NTM-LD (n = 19), or non-infectious inflammatory disease (n = 4). We applied depletion of human cells, removal of extracellular DNA, implementation of a decontamination strategy, and exploratory whole-metagenome sequencing (WMS) of selected specimens.

RESULTS: Genera Serratia and unclassified Yersiniaceae dominated the lung microbiome of most patients with a mean relative abundance of >15% and >70%, respectively. However, at the sub-genus level, as determined by amplicon sequence variants (ASVs), TB-patients exhibited increased community diversity, and distinct signatures of ASV_7, ASV_21 abundances which resulted in a significant association with disease state. Exploratory WMS, and ASV similarity analyses suggested the presence of Serratia liquefaciens, Serratia grimesii, Serratia myotis and/or Serratia quinivorans in TB and NTM-LD patients.

CONCLUSIONS: The lung microbiome of TB-patients harbored a distinct, and heterogenous structure, with specific occurrences of certain Serratia traits. Some of these traits may play a role in understanding the microbial interactions in the lung microbiome of patients infected with Mtbc.}, } @article {pmid40569694, year = {2025}, author = {Kasmanas, JC and Magnúsdóttir, S and Zhang, J and Smalla, K and Schloter, M and Stadler, PF and de Leon Ferreira de Carvalho, ACP and Rocha, U}, title = {Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40569694}, issn = {2047-217X}, support = {2019/03,396-9//São Paulo Research Foundation/ ; 2022/03,534-5//São Paulo Research Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; //International Development Research Centre/ ; }, mesh = {*Plasmids/genetics ; Humans ; *Genomics/methods ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Virulence Factors/genetics ; Computational Biology/methods ; Software ; Genome, Bacterial ; *Bacteria/genetics/pathogenicity/drug effects ; }, abstract = {BACKGROUND: Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics' impact on public health. gSpreadComp streamlines the path from in silico analysis to hypothesis generation. By integrating comparative genomics, genome annotation, normalization, plasmid-mediated gene transfer, and microbial resistance-virulence risk-ranking into a unified workflow, gSpreadComp facilitates hypothesis generation from complex microbial datasets.

FINDINGS: The gSpreadComp workflow works through 6 modular steps: taxonomy assignment, genome quality estimation, antimicrobial resistance (AMR) gene annotation, plasmid/chromosome classification, virulence factor annotation, and downstream analysis. Our workflow calculates gene spread using normalized weighted average prevalence and ranks potential resistance-virulence risk by integrating microbial resistance, virulence, and plasmid transmissibility data and producing an HTML report. As a use case, we analyzed 3,566 metagenome-assembled genomes recovered from human gut microbiomes across diets. Our findings indicated consistent AMR across diets, with diet-specific resistance patterns, such as increased bacitracin in vegans and tetracycline in omnivores. Notably, ketogenic diets showed a slightly higher resistance-virulence rank, while vegan and vegetarian diets encompassed more plasmid-mediated gene transfer.

CONCLUSIONS: The gSpreadComp workflow aims to facilitate hypothesis generation for targeted experimental validations by the identification of concerning resistant hotspots in complex microbial datasets. Our study raises attention to a more thorough study of the critical role of diet in microbial community dynamics and the spread of AMR. This research underscores the importance of integrating genomic data into public health strategies to combat AMR. The gSpreadComp workflow is available at https://github.com/mdsufz/gSpreadComp/.}, } @article {pmid40568985, year = {2025}, author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {Quantifying the contribution of the rare biosphere to natural disturbances.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40568985}, issn = {1751-7370}, support = {OCE 1416673 and DEB 1831582//US National Science Foundation/ ; ICER 2033934, DEB 2224819//US National Science Foundation/ ; }, mesh = {Metagenome ; *Ecosystem ; *Microbiota ; }, abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e. the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e. disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.}, } @article {pmid40568302, year = {2025}, author = {Ostrzinski, A and Kunath, BJ and Soares, AR and Laczny, CC and Halder, R and Kallmeyer, J and di Primio, R and Wilmes, P and Probst, AJ and Trautwein-Schult, A and Becher, D}, title = {Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf074}, pmid = {40568302}, issn = {2730-6151}, abstract = {Marine sediments harbor extremely diverse microbial communities that contribute to global biodiversity and play an essential role in the functioning of ecosystems. However, the metaproteome of marine sediments is still poorly understood. The extraction of proteins from environmental samples is still a challenge, especially from marine sediments, due to the complexity of the matrix. Therefore, methods for protein extraction from marine sediments need to be improved. To develop an effective workflow for protein extraction for clayey sediments, we compared, combined and enhanced different protein extraction methods. The workflow presented here includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis by ultrasonic capture, electro-elution, and simultaneous fractionation of proteins. To test the protocol's efficacy, we added Escherichia coli cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of E. coli proteins from the supplemented sediment to those from pure E. coli cultures. This new protocol will enable future studies to identify active players in clay-rich marine sediments and accurately determine functional biodiversity based on their respective protein complements.}, } @article {pmid40566942, year = {2025}, author = {Kara, K and Yilmaz Öztaş, S and Baytok, E}, title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.}, journal = {Veterinary medicine and science}, volume = {11}, number = {4}, pages = {e70447}, pmid = {40566942}, issn = {2053-1095}, support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; }, mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; }, abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.

OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.

METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24 h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.

RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p < 0.05). Thyme pulp exhibited the highest NH3-N levels (75.14 mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93 mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p < 0.05).

CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.}, } @article {pmid40565014, year = {2025}, author = {Monareng, NJ and Ncube, KT and van Rooi, C and Modiba, MC and Mtileni, B}, title = {A Systematic Review on Microbial Profiling Techniques in Goat Milk: Implications for Probiotics and Shelf-Life.}, journal = {International journal of molecular sciences}, volume = {26}, number = {12}, pages = {}, pmid = {40565014}, issn = {1422-0067}, support = {PMDS240528221992//National Research Foundation/ ; }, mesh = {Goats ; Animals ; *Milk/microbiology ; *Probiotics ; *Microbiota ; *Food Microbiology ; Humans ; }, abstract = {Due to its high digestibility, rich nutrient profile, and potential probiotic content, goat milk is an essential nutritional resource, particularly for individuals with cow milk allergies. This review summarises the current state of microbial diversity in goat milk, emphasising the implications for quality, safety, and probiotic potential. This systematic review adhered to PRISMA guidelines, conducting a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar using keywords related to microbial profiling in goat milk. The inclusion criteria targeted English-language studies from 2000 to 2025 that utilised high-throughput or next-generation sequencing methods. Out of 126 articles screened, 84 met the eligibility criteria. The extracted data focused on microbial diversity, profiling techniques, and their respective strengths and limitations in evaluating probiotic potential and spoilage risks. The review addresses the challenges linked to microbial spoilage and the composition and functional roles of microbial communities in goat milk. With species such as Bacillus and Pseudomonas playing crucial roles in fermentation and spoilage, key findings emphasise the prevalence of microbial phyla, including Proteobacteria, Firmicutes, and Actinobacteria in goat milk. The review also explores the probiotic potential of the goat milk microbiota, highlighting the health benefits associated with strains such as Lactobacillus and Bifidobacterium. Significant discoveries underline the necessity for advanced multi-omics techniques to thoroughly define microbial ecosystems and the substantial gaps in breed-specific microbiota research. Important findings illustrate the need for enhanced multi-omics techniques, given the challenges of host RNA and protein interference, low microbial biomass, and limited goat-specific reference databases, for optimising probiotic development, spoilage prevention strategies, and integrating metagenomics, metabolomics, metaproteomics, and metatranscriptomics to improve milk quality and safety as some of the future research objectives. This study emphasises the importance of understanding goat milk microbiology to advance dairy science and enhance human health.}, } @article {pmid40563104, year = {2025}, author = {Trutschel, L and Kruger, B and Czaja, A and Brueck, M and Sackett, J and Druschel, G and Rowe, A}, title = {Sulfide Oxidation Products Support Microbial Metabolism at Interface Environments in a Marine-Like Serpentinizing Spring in Northern California.}, journal = {Geobiology}, volume = {23}, number = {4}, pages = {e70026}, pmid = {40563104}, issn = {1472-4669}, support = {80NSSC21K0482/NASA/NASA/United States ; }, mesh = {Oxidation-Reduction ; California ; *Sulfides/metabolism ; *Bacteria/metabolism/classification/genetics ; *Natural Springs/microbiology/chemistry ; Microbiota ; }, abstract = {Interface environments between extreme and neutrophilic conditions are often hotspots of metabolic activity and taxonomic diversity. In serpentinizing systems, the mixing of high pH fluids with meteoric water, and/or the exposure of these fluids to the atmosphere can create interface environments with distinct but related metabolic activities and species. Investigating these systems can provide insights into the factors that stimulate microbial growth, and/or what attributes may be limiting microbial physiologies in native serpentinized fluids. To this aim, changes in geochemistry and microbial communities were investigated for different interface environments at Ney Springs-a marine-like terrestrial serpentinization system where the main serpentinized fluids have been well characterized geochemically and microbially. We found that reduced sulfur species from Ney Springs had large impacts on the community changes observed at interface environments. Oxygen availability at outflow environments resulted in a relative increase in the taxa observed that were capable of sulfur oxidation, and in some cases light-driven sulfur oxidation. A combination of cultivation work and metagenomics suggests these groups seem to predominantly target sulfur intermediates like polysulfide, elemental sulfur, and thiosulfate as electron donors, which are present and abundant to various degrees throughout the Ney system. Fluid mixing with meteoric water results in more neutral pH systems which in turn select for different sulfur-oxidizing taxa. Specifically, we see blooms of taxa that are not typically observed in the primary Ney fluids, such as Halothiobacillus in zones where fluids mix underground with meteoric water (~pH 10) or the introduction of Thiothrix into the nearby creek as fluids enter at the surface (~pH 8). This work points to the potential importance of oxidants for stimulating microbial respiration at Ney Springs, and the observation that these serpentinized fluids act as an important source of reduced sulfur, supporting diverse taxa around the Ney Springs system.}, } @article {pmid40562089, year = {2025}, author = {Gu, P and Xu, Y and Li, X}, title = {Chronic low-dose cadmium exposure disrupts gut microbiota and lipid metabolism to induce liver injury.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {203}, number = {}, pages = {115603}, doi = {10.1016/j.fct.2025.115603}, pmid = {40562089}, issn = {1873-6351}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Cadmium/toxicity/administration & dosage ; Mice ; Male ; Mice, Inbred C57BL ; Liver/drug effects/metabolism/pathology ; *Chemical and Drug Induced Liver Injury/metabolism/microbiology ; }, abstract = {Cadmium (Cd) is a widespread environmental pollutant linked to liver injury and metabolic dysfunction, yet the gut-liver axis mechanisms remain unclear. We investigated chronic low-dose Cd exposure (100 nM CdCl2, 12 weeks) in mice using integrated metagenomic and metabolomic profiling. Despite intact intestinal morphology, Cd exposure induced hepatic inflammation, steatosis, and elevated transaminases. Shotgun metagenomics revealed gut microbiota shifts, with enrichment of Prevotella and depletion of Turicibacter. Fecal metabolomics showed disrupted bile acid detoxification and lipid remodeling. Functional analysis indicated upregulation of microbial fatty acid metabolism genes, suggesting compensatory but dysregulated responses. These findings demonstrate that chronic Cd exposure perturbs gut microbiota and metabolic outputs, driving liver injury via microbiota-mediated mechanisms. Our study highlights the gut-liver axis as a key target of Cd toxicity and points to microbiota-based interventions as potential therapies.}, } @article {pmid40560512, year = {2025}, author = {Pramanik, K and Sen, A and Dutta, S and Mandal, GS and Paramanik, B and Das, A and Chatterjee, N and Ghorai, AK and Ali, MN}, title = {Microbial populations under fluoride stress: a metagenomic exploration from Indian soil.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {7}, pages = {221}, pmid = {40560512}, issn = {1573-0972}, mesh = {*Soil Microbiology ; *Fluorides/analysis ; India ; Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Soil/chemistry ; Fungi/genetics/classification/drug effects/isolation & purification ; Archaea/genetics/classification/drug effects/isolation & purification ; Metagenome ; Phylogeny ; Microbiota/drug effects ; }, abstract = {Fluoride exposure, even at a low concentration, significantly impairs crop growth and productivity by inhibiting metabolic enzymes and disrupting photosynthesis. Addressing this challenge, microbial de-fluoridation emerges as a vital strategy to improve soil health, enhance crop growth, and ensure agricultural sustainability. This study analyzed topsoil samples (0-0.2 m depth) from rice fields in three blocks of Purulia district, West Bengal-Arsha, Jhalda-I, and Joypur. Fluoride content in the samples ranged from 58.76 ± 0.76 mg/kg to 282.9 ± 4.9 mg/kg (total) and 1.57 ± 0.02 mg/kg to 2.97 ± 0.03 mg/kg (available). The metagenomic analysis of the collected soil samples revealed diverse microbial communities comprising archaea, bacteria, fungi, and viruses, with Actinobacteria (phylum), Hyphomicrobiales (order), and Nocardioidaceae (family) being the dominant prokaryotes. Arsha soil with comparatively low fluoride contamination exhibited the highest microbial diversity (11,891 taxa), followed by Joypur (11,528 taxa) and Jhalda-I (11,358 taxa), with Arsha showing nearly double the unique microbial taxa compared to the other locations. Clusters of orthologous groups of proteins functional analysis identified 60,898 genes in Arsha, 63,403 genes in Jhalda-I, and 73,334 genes in Joypur, while Kyoto encyclopedia of genes and genomes analysis revealed 9,385, 9,104, and 10,633 genes, respectively. Key genes associated with fluoride metabolism-inorganic pyrophosphatase, divalent metal cation transporter mntH, and putative fluoride ion transporter crcB-were abundant across all sites, highlighting the influence of fluoride on microbial community structure. This study provides the first comprehensive report on soil microbial communities in fluoride-rich areas, highlighting the potential of native fluoride-tolerant microbes to mitigate fluoride toxicity in agricultural soils and offer sustainable, microbe-based solutions to fluoride contamination.}, } @article {pmid40559651, year = {2025}, author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M}, title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.}, journal = {Marine drugs}, volume = {23}, number = {6}, pages = {}, pmid = {40559651}, issn = {1660-3397}, support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation & purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; }, abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.}, } @article {pmid40558870, year = {2025}, author = {Abreu, CM and Carneiro, GHF and Costa, MRD and Barroso, GM and Duque, TS and Silva, JMS and Santos, JBD}, title = {Avena sativa as a Multifunctional Tool for Phytoremediation and Bioenergy Production in Sulfentrazone Contaminated Soils.}, journal = {Journal of xenobiotics}, volume = {15}, number = {3}, pages = {}, pmid = {40558870}, issn = {2039-4713}, support = {APQ 01151-23; APQ 00694-23 and, APQ 004955-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//National Council for Scientific and Technological Development/ ; }, abstract = {Phytoremediation using Avena sativa offers a sustainable strategy for mitigating sulfentrazone contamination while integrating bioenergy production. This study proposes an analysis of the bioenergy potential and the microbial metagenomic profile associated with Avena sativa in the presence and absence of sulfentrazone, aiming at the synergistic bioprospecting of microbial communities capable of biodegradation and remediation of contaminated environments. Using a randomized block design, we evaluated the bioenergy potential and rhizospheric microbial dynamics of A. sativa in soils with and without sulfentrazone (600 g ha[-1]). Herbicide residues were quantified via UHPLC-MS/MS, and metagenomic profiles were obtained through 16S rRNA gene and ITS region sequencing to assess shifts in rhizospheric microbiota. Microbial diversity was analyzed using the Shannon and Gini-Simpson Indices, complemented by Principal Component Analysis (PCA). Bioenergy yields (biogas and ethanol) were estimated based on plant biomass. Over 80 days, the cultivation of A. sativa promoted a 19.7% dissipation of sulfentrazone, associated with rhizospheric enrichment of plant growth-promoting taxa (Bradyrhizobium, Rhodococcus, and Trichoderma), which increased by 68% compared to uncontaminated soils. Contaminated soils exhibited reduced microbial diversity (Gini-Simpson Index = 0.7), with a predominance of Actinobacteria and Ascomycota, suggesting adaptive specialization. Despite herbicide-induced stress (39.3% reduction in plant height and 60% reduction in grain yield), the biomass demonstrated considerable bioenergy potential: 340.6 m[3] ha[-1] of biogas and 284.4 L ha[-1] of ethanol. The findings highlight the dual role of A. sativa in soil rehabilitation and renewable energy systems, supported by plant-microbe synergies. Scalability challenges and regulatory gaps in ecotoxicological assessments were identified, reinforcing the need to optimize microbial consortia and implement region-specific management strategies. These results support the integration of phytoremediation into circular bioeconomy models, balancing ecological recovery with agricultural productivity. Future research should focus on microbial genetic pathways, field-scale validation, and the development of regulatory frameworks to advance this green technology in global soil remediation efforts.}, } @article {pmid40558050, year = {2025}, author = {Phan, J and Jain, S and Nijkamp, JF and Sasidharan, R and Agarwal, A and Bird, JK and Spooren, A and Wittwer Schegg, J and Ver Loren van Themaat, E and Mak, TN}, title = {Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0027125}, pmid = {40558050}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/microbiology/diagnosis ; *Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Adult ; Cross-Sectional Studies ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; *Gastrointestinal Tract/microbiology ; Phenotype ; Gastrointestinal Diseases/microbiology ; Young Adult ; Metagenomics/methods ; }, abstract = {Despite the complexity of the gut microbiome, several scores that use taxonomic characteristics exist that attempt to identify a healthy gut or gastrointestinal disease. Two systems in use are the metagenomic aerotolerant predominance index (MAPI) and keystone scores. The aim of this analysis was to compare different gut microbiome scores, specifically MAPI and a keystone species score, on two cross-sectional data sets and to investigate correlations of these scores with self-reported gut discomfort and gastrointestinal disease. The first data set is a commercial data set (Sun Genomics data set) with whole-genome shotgun sequencing samples from 5,372 customers. The second data set is curated from publicly available data (public data set) with 2,415 samples from participants in human studies with gut-related taxonomic profiles. MAPI scores and keystone species scores were calculated using standard methodology. The MAPI score was significantly lower in men for the public data set. There was a graded response for both the MAPI and keystone scores between healthy subjects, subjects with mild gastrointestinal discomfort, and patients with gastrointestinal disease: the MAPI score was higher, and the keystone score was lower in subjects with gastrointestinal discomfort or with inflammatory bowel disease patients. The keystone and MAPI scores have the potential to help identify factors associated with gut microbial dysbiosis and gastrointestinal discomfort or disease. Furthermore, given the functional link of the MAPI score to oxidative stress in the microbiome, the scores can help to identify conditions where oxidative stress is one of the hallmarks of dysbiosis.IMPORTANCEGut bacteria play a role in both mild gastrointestinal discomfort, which includes bloating and constipation, and inflammatory bowel disease. There are many different types of bacteria in the gut, and gut microbiome composition differs greatly between different people. Therefore, it is difficult to predict who has a gut microbiome associated with a healthy gut and who might develop disease or experience gut discomfort. Several scoring systems have been developed to categorize gut health states. This analysis compared two different scoring systems using data from two different sources to see how well they could identify people with gastrointestinal disease, gastrointestinal complaints, or a healthy gut. The scoring systems showed similar trends according to gut health status: groups of people with gut bacteria imbalance or gut disease had a different score than groups of people with healthy gut bacteria.}, } @article {pmid40557789, year = {2025}, author = {Jones, KS and Pilliod, DS and Aunins, AW}, title = {Metabarcoding Analysis of Arthropod Pollinator Diversity: A Methodological Comparison of eDNA Derived From Flowers and DNA Derived From Bulk Samples of Insects.}, journal = {Molecular ecology}, volume = {34}, number = {14}, pages = {e70003}, doi = {10.1111/mec.70003}, pmid = {40557789}, issn = {1365-294X}, support = {//U.S. Bureau of Land Management/ ; //U.S. Geological Survey/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Pollination ; *Flowers/genetics ; Bees/genetics/classification ; *Biodiversity ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; Sequence Analysis, DNA ; *Insecta/genetics/classification ; }, abstract = {Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.}, } @article {pmid40557154, year = {2025}, author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M}, title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1555441}, pmid = {40557154}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; }, abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.

METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.

RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.

CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.}, } @article {pmid40556381, year = {2025}, author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z}, title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {27}, pages = {17219-17232}, doi = {10.1021/acs.jafc.5c02308}, pmid = {40556381}, issn = {1520-5118}, mesh = {Fermentation ; *Flavoring Agents/metabolism/chemistry ; *Guanidines/analysis/metabolism ; *Bacteria/genetics/isolation & purification/classification/metabolism ; Microbiota/drug effects ; Volatile Organic Compounds/chemistry/metabolism ; *Nitro Compounds/analysis/metabolism ; Gas Chromatography-Mass Spectrometry ; *Neonicotinoids/analysis ; *Pesticide Residues/analysis ; Taste ; Odorants/analysis ; *Fermented Foods/microbiology/analysis ; Metagenomics ; *Brassica/microbiology/chemistry ; }, abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.}, } @article {pmid40555791, year = {2025}, author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y}, title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.}, journal = {Nature microbiology}, volume = {10}, number = {7}, pages = {1684-1697}, pmid = {40555791}, issn = {2058-5276}, mesh = {*Ammonia/metabolism ; *Renal Insufficiency, Chronic/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Mice ; Humans ; Aged ; Aged, 80 and over ; Escherichia coli/genetics/metabolism ; Male ; Female ; Metagenome ; Kidney ; Mice, Inbred C57BL ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.}, } @article {pmid40555747, year = {2025}, author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ}, title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {867}, pmid = {40555747}, issn = {2399-3642}, mesh = {Humans ; *Bifidobacterium/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; }, abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.}, } @article {pmid40555025, year = {2025}, author = {Lin, Z and Pang, S and Wu, Y and Xu, T and Zhou, YL and Li, H and Zhang, C and Qian, PY and Zhang, S}, title = {Biodiversity and nitrogen metabolism in the plastisphere impacted by urban nitrogen loading from a coastal mega-city.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139012}, doi = {10.1016/j.jhazmat.2025.139012}, pmid = {40555025}, issn = {1873-3336}, abstract = {The plastisphere, recognized for vast biomass and critical role in nitrogen cycling, is becoming a pertinent component of marine ecosystems. The relationship between plastisphere and increased nitrogen inputs from urban wastewater in coastal zones remains poorly understood. Through metagenomics, metatranscriptomics and metabolomics, this research sought to elucidate the plastisphere's reaction to elevated nitrogen loading and pinpoint key microbial resources that can be harnessed. Although the archaeal community composition within the plastisphere remains largely unchanged by nitrogen loading, bacterial diversity experiences a substantial boost, which is inversely correlated with fungal diversity. Furthermore, such conditions are associated with reduced intricate microbial interactions. Moreover, the plastisphere subjected to nitrogen loading shows an enrichment of genera and genes implicated in ammonium assimilation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Metabolomics analysis highlighted the plastisphere's accumulation of L-glutathione oxidized (GSSG) in response to nitrogen loading. The research further highlighted a quartet of microbial phyla-Actinomycetota, Bacteroidota, Cyanobacteriota, and Pseudomonadota-that not only thrive but also constitute pivotal microbial resources within the plastisphere when confronted with strong nitrogen loading. In essence, this investigation illuminates the plastisphere's biodiversity dynamics and nitrogen metabolic adjustments during augmented nitrogen loading and offers novel perspectives on taking advantage of the plastisphere's untapped microbial potential.}, } @article {pmid40554894, year = {2025}, author = {Zheng, SJ and Gao, XY and Diao, XH and Chen, ND}, title = {Dendrobium huoshanense improves atherosclerosis in high-fat-induced ApoE mice by regulating gut microbiota and serum metabolite profiles.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {156964}, doi = {10.1016/j.phymed.2025.156964}, pmid = {40554894}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dendrobium/chemistry ; *Atherosclerosis/drug therapy/metabolism ; Mice ; Male ; *Polysaccharides/pharmacology ; NF-E2-Related Factor 2/metabolism ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Reactive Oxygen Species/metabolism ; Matrix Metalloproteinase 9/metabolism ; Malondialdehyde/metabolism ; Feces/microbiology ; Heme Oxygenase-1/metabolism ; Apolipoproteins E ; Matrix Metalloproteinase 2/metabolism ; Disease Models, Animal ; Antioxidants/pharmacology ; Superoxide Dismutase/metabolism ; Plant Extracts/pharmacology ; Membrane Proteins ; }, abstract = {BACKGROUND: Cardiovascular diseases, particularly atherosclerosis (AS), remain leading causes of mortality, with limited effective treatments available. Dendrobium huoshanense, a traditional medicinal herb, has shown promising anti-inflammatory and antioxidant effects, but its cardiovascular protective potential remains underexplored.

PURPOSE: This study aimed to explore the protective effects of Dendrobium huoshanense polysaccharides (DHP) against AS and elucidate the underlying mechanisms involved.

METHODS: An ApoE(-/-) mice model of AS was established, and DHP was administered at different concentrations via gavage. After 14 weeks, serum and fecal samples were collected. The effects of DHP on lipid profiles, aortic plaques, matrix metalloproteinases (MMP-2 and MMP-9), and the Nrf2/HO-1 pathway were assessed. Additionally, metagenomic sequencing of fecal samples and untargeted metabolomics of serum were conducted and correlations between these findings were explored.

RESULTS: DHP improved lipid profiles, reduced reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and enhanced superoxide dismutase (SOD) activity. It stabilized aortic plaques, suppressed MMP-2 and MMP-9 overexpression, and activated the Nrf2/HO-1 pathway. DHP also promoted gut microbiota balance, increasing Mucispirillum, Bifidobacterium, and Faecalibaculum while decreasing Desulfovibrionaceae and Eubacterium. Metabolomics revealed alterations in metabolites, including taurochenodeoxycholic acid and ursocolic acid, influencing amino acid, glycerophospholipid, and bile acid metabolism.

CONCLUSIONS: DHP effectively lowers lipid levels, stabilizes aortic plaques, restores gut microbiota balance, and corrects metabolic disturbances, thereby inhibiting the progression of atherosclerosis. These findings provide a scientific basis for the clinical use of DHP in AS prevention and treatment.}, } @article {pmid40554148, year = {2025}, author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y}, title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.}, journal = {Water research}, volume = {284}, number = {}, pages = {123973}, doi = {10.1016/j.watres.2025.123973}, pmid = {40554148}, issn = {1879-2448}, mesh = {*Wastewater ; *Ethanol/metabolism ; *Lactic Acid/metabolism ; *Microbial Consortia ; *Caproates/metabolism ; Fermentation ; }, abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.}, } @article {pmid40553325, year = {2025}, author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P}, title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2952}, number = {}, pages = {15-37}, pmid = {40553325}, issn = {1940-6029}, mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; }, abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.}, } @article {pmid40552763, year = {2025}, author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF}, title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2520412}, doi = {10.1080/19490976.2025.2520412}, pmid = {40552763}, issn = {1949-0984}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; *Clostridioides difficile/physiology ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Recurrence ; }, abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.}, } @article {pmid40551486, year = {2025}, author = {Yan, F and Wu, SM and Yuan, WQ and Yang, YH and Zhu, H and Cui, DJ}, title = {Thermophiles, Thick-Walled Bacteria, and Pseudomonads in High-Altitude Gut Microbiota.}, journal = {Journal of gastroenterology and hepatology}, volume = {40}, number = {8}, pages = {1976-1990}, doi = {10.1111/jgh.17032}, pmid = {40551486}, issn = {1440-1746}, support = {qiankehe2018-5764-11//Cultivation Fund of National Natural Science Foundation/ ; gzwkj2025-268//Science and Technology Fund of Guizhou provincial health committee/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; Bone Morphogenetic Protein 4/metabolism/genetics ; Glycolysis/genetics ; *Altitude ; Intestinal Mucosa/metabolism/microbiology ; Mice, Inbred C57BL ; Male ; Down-Regulation ; Cell Communication ; Hypoxia ; Mice ; Fibroblasts/metabolism ; Epithelial Cells/metabolism ; Butyrates/metabolism ; }, abstract = {BACKGROUND AND AIM: High-altitude environments are characterized by low oxygen and reduced low pressure, which impose significant physiological challenges on organisms. Among various adaptive systems, the intestinal flora plays a crucial role in maintaining gut health and barrier integrity function under such conditions. This study aimed to elucidate the regulatory mechanisms of intestinal flora in high-altitude environments, focusing on downregulating intracellular Bone Morphogenetic Protein 4 (BMP4) to influence glycolysis metabolism, thereby affecting intercellular communication of the intestinal mucosal barrier and matrix remodeling.

METHODS: High-altitude mouse intestinal flora composition and function were analyzed using 16S rRNA and metagenomic sequencing. Additionally, single-cell sequencing was employed to examine cell population communication and gene expression differences between normal and high-altitude mouse intestinal tissues.

RESULTS: Single-cell sequencing showed significantly reduced interactions between intestinal fibroblasts and epithelial cells in high-altitude mice, accompanied by a marked increase in BMP4 expression. Overexpression of BMP4 was found to activate the glycolysis pathway. Gut microbiota metabolites, including secondary bile acids, lactic acid, and butyrate, exhibited protective effects on hypoxia-induced intestinal mucosal barrier injury, with butyrate showing the most prominent effect. Under hypoxic conditions, butyrate suppressed the BMP4/glycolysis pathway, thereby alleviating hypoxia-induced intestinal mucosal barrier damage.

CONCLUSION: This study uncovered a novel mechanism by which the gut microbiota in high-altitude environments modulate glycolysis metabolism through BMP4 downregulation, thereby affecting intercellular communication and matrix remodeling within the intestinal mucosal barrier.}, } @article {pmid40550680, year = {2025}, author = {Lin, M and Hu, L and Hao, L and Wang, Z}, title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {6}, pages = {2415-2431}, doi = {10.13345/j.cjb.240399}, pmid = {40550680}, issn = {1872-2075}, mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; }, abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.}, } @article {pmid40550672, year = {2025}, author = {Wang, X and Wang, S and Yang, K and Tang, Y and Xu, Y and Shen, Q and Wei, Z}, title = {[Methodological breakthroughs and challenges in research of soil phage microecology].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {6}, pages = {2310-2323}, doi = {10.13345/j.cjb.250258}, pmid = {40550672}, issn = {1872-2075}, mesh = {*Bacteriophages/genetics/isolation & purification/physiology ; *Soil Microbiology ; Ecosystem ; Microbiota ; Metagenomics/methods ; }, abstract = {Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators in Earth's ecosystems, driving biogeochemical cycles, energy fluxes, and ecosystem services across terrestrial and marine environments. Within soil microbiomes, phages function as microbial "dark matter," maintaining the soil-plant system balance through precise modulation of the microbial community structure and functional dynamics. Despite the growing research interests in soil phages in recent years, the proportion of such studies in environmental virology remains disproportionately low, which is primarily attributed to researchers' limited familiarity with the research methodologies for phage microecology, incomplete technical frameworks, and inherent challenges posed by soil environmental complexity. To address these challenges, this review synthesizes cutting-edge methodologies for soil phage investigation from four aspects: (1) tangential flow filtration (TFF)-based phage enrichment strategies; (2) integrated quantification approaches combining double-layer agar plating, epifluorescence microscopy, and flow cytometry; (3) multi-omics analytical pipelines leveraging metagenomics and viromics datasets; and (4) computational frameworks merging machine learning algorithms with eco-evolutionary theory for deciphering phage-host interaction networks. Through comparative analysis of methodological principles, technical merits, and application scopes, we establish a comprehensive workflow for soil phage research. Future research in this field should prioritize: (1) construction of soil phage resource libraries, (2) exploration of RNA phages based on transcriptomes, (3) functional characterization of unknown genes, and (4) deep integration and interaction validation of multi-omics data. This systematic methodological synthesis provides critical technical references for addressing fundamental challenges in characterizing soil phages regarding the community structure, functional potential, and interaction mechanisms with hosts.}, } @article {pmid40548332, year = {2025}, author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {283}, pmid = {40548332}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).}, } @article {pmid40544519, year = {2025}, author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y}, title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.}, journal = {Polish journal of microbiology}, volume = {74}, number = {2}, pages = {192-205}, pmid = {40544519}, issn = {2544-4646}, mesh = {Humans ; Infant ; *High-Throughput Nucleotide Sequencing ; Male ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; Intensive Care Units, Pediatric ; *Trachea/microbiology ; *Pneumonia/microbiology/diagnosis/virology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; Coinfection/microbiology ; }, abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.}, } @article {pmid40543204, year = {2025}, author = {Yang, J and Kim, JS and Jeon, HW and Lee, J and Seo, JH}, title = {Integrated culture-based and metagenomic profiling of airborne and surface-deposited bacterial communities in residential environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126703}, doi = {10.1016/j.envpol.2025.126703}, pmid = {40543204}, issn = {1873-6424}, mesh = {*Air Microbiology ; *Air Pollution, Indoor/analysis/statistics & numerical data ; *Bacteria/genetics/classification/isolation & purification ; *Environmental Monitoring ; Housing ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Humans ; }, abstract = {Indoor environments host diverse microbial communities, where airborne and surface-deposited bacteria contribute to human exposure and potential health risks. This study applies metagenomic analysis to examine bacterial diversity in residential apartments, focusing on four key indoor spaces: kitchens, living rooms, toilets, and bedrooms. Airborne bacteria were collected using a culture-based air sampler and surface-deposited bacteria were collected via swabbing of high-contact areas; both were analyzed through 16S rRNA gene sequencing and bioinformatics processing. Airborne bacterial communities were primarily composed of Staphylococcus, Bacillus, and Enhydrobacter, whereas surface-deposited bacteria varied by location, with Streptococcus and Staphylococcus being most common on high-contact surfaces. Overall, surface-deposited bacterial diversity was greater than that of airborne communities, highlighting their distinct but interconnected roles in indoor microbial ecosystems. Functional pathway analysis suggested that indoor bacterial communities may harbor metabolic functions, as well as antibiotic resistance and virulence-related pathways, pointing to potential health concerns. Principal component analysis (PCA) showed clear distinctions between airborne and surface-deposited bacterial communities. These findings highlight the need for space-specific microbial management strategies, such as improved ventilation and surface hygiene, to reduce exposure risks and promote healthier indoor environments.}, } @article {pmid40542451, year = {2025}, author = {Ji, S and Ahmad, F and Peng, B and Yang, Y and Su, M and Zhao, X and Vatanen, T}, title = {Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {149}, pmid = {40542451}, issn = {2049-2618}, support = {U22A20365//Joint Funds of National Natural Science Foundation of China/ ; T2341019//National Natural Science Foundation of China/ ; 2023A1515012429//Natural Science Foundation of Guangdong Province/ ; 2024B03J1343//Guangzhou Science and Technology Plan Project/ ; }, mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/virology ; Bacteria/metabolism/virology/genetics/classification ; Metagenome ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.

METHODS: The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.

RESULTS: Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.

CONCLUSIONS: FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.}, } @article {pmid40542420, year = {2025}, author = {Yu, M and Chu, Y and Wang, Y and Mo, L and Tan, X and Guo, S and Yuan, S and Ma, Y}, title = {Metagenomic analysis reveals gut phage diversity across three mammalian models.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {146}, pmid = {40542420}, issn = {2049-2618}, support = {2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; B2302023//Shenzhen Medical Research Fund/ ; B2302023//Shenzhen Medical Research Fund/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Swine ; *Bacteriophages/genetics/classification/isolation & purification ; Mice ; Humans ; Macaca fascicularis/virology ; Metagenome ; Virome ; Phylogeny ; Models, Animal ; Feces/virology ; }, abstract = {BACKGROUND: The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.

RESULTS: We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.

CONCLUSIONS: Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.}, } @article {pmid40542287, year = {2025}, author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C}, title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.}, journal = {Nature microbiology}, volume = {10}, number = {7}, pages = {1570-1580}, pmid = {40542287}, issn = {2058-5276}, support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; }, mesh = {*Microbiota/genetics ; Humans ; Biomass ; *Metagenomics/methods/standards ; Specimen Handling/standards/methods ; *DNA Contamination ; Guidelines as Topic ; }, abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.}, } @article {pmid40541587, year = {2025}, author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TT and Dawson, HD}, title = {Broccoli Consumption Alters Microbial Diversity, Metatranscriptome, and Host Transcriptome in Mice Fed a Total Western Diet.}, journal = {The Journal of nutrition}, volume = {155}, number = {8}, pages = {2545-2559}, doi = {10.1016/j.tjnut.2025.05.041}, pmid = {40541587}, issn = {1541-6100}, mesh = {Animals ; *Brassica ; Male ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; *Diet, Western ; *Transcriptome ; Mice ; Cecum/microbiology ; }, abstract = {BACKGROUND: Cruciferous vegetables (CVs) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent cruciferous vegetable compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) is unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.

OBJECTIVES: We investigated the effects of broccoli powder (BP)-supplemented total Western diet (TWD) on changes in the gut microbiome, the host transcriptome, and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.

METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for 6 wk followed by supplementation with 0%, 0.5%, 1%, or 2.5% BP (reflecting a human intake from ¼-1 cup/d) for 3 wk. Microbial communities from cecal contents were taxonomically profiled using 16S ribosomal ribonucleic acid amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess the functionality of the microbial communities. The host cecal transcriptome was also assessed.

RESULTS: β-diversity was significantly higher (P = 1.20 × 10[-3]) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial ribonucleic acid transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation, and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.

CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host, and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.}, } @article {pmid40541123, year = {2025}, author = {Jiao, Y and Xiao, D and Li, X and Jiang, M and Li, H}, title = {Integrative fMRI and multiomics reveal neuroprotective mechanisms of Astragalus membranaceus in sleep deprivation-induced depression.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {156959}, doi = {10.1016/j.phymed.2025.156959}, pmid = {40541123}, issn = {1618-095X}, mesh = {Random Allocation ; Male ; Animals ; Mice ; Mice, Inbred C57BL ; *Astragalus propinquus/chemistry ; Plant Extracts/chemistry/pharmacology/therapeutic use ; Phytotherapy ; *Neuroprotective Agents/analysis/pharmacology/therapeutic use ; *Sleep Deprivation/complications/microbiology ; *Depression/diagnostic imaging/drug therapy/metabolism/microbiology ; Magnetic Resonance Imaging ; Multiomics ; *Brain-Gut Axis/drug effects ; Transcriptome ; *Brain/diagnostic imaging/drug effects/metabolism ; Dysbiosis/complications/drug therapy/microbiology ; Gastrointestinal Microbiome/drug effects ; }, abstract = {BACKGROUND: Sleep deprivation (SD) is a significant public health concern and a risk factor for neuropsychiatric disorders, including depression. SD disrupts the gut-brain axis, causing dysbiosis and neuroinflammation. Astragalus membranaceus (AST) exhibits antidepressant and anti-inflammatory properties, including modulation of the gut microbiota; however, its neuroprotective effects on SD-induced neuropsychiatric disturbances remain largely unexplored. This study investigates the potential of AST using an innovative integrative multiomics approach.

PURPOSE: This study was conducted to investigate the neuroprotective effects of AST against SD-induced depression-like behavior and to explore the mechanism underlying its regulatory effects on the gut-brain axis.

METHODS: We established a chronic SD mouse model that was subjected to AST intervention and employed a pioneering integrative multiomics approach-combining resting-state functional magnetic resonance imaging for brain function, metagenomics for microbiota profiling, metabolomics for metabolic alterations, and transcriptomics for gene expression in key brain regions. Behavioral tests and cytokine assays complemented these analyses to comprehensively evaluate the therapeutic effects of AST.

RESULTS: SD induced depression-like behavior, neuroinflammation (IL-1β, IL-6, and TNF-α secretion), gut dysbiosis (Proteobacteria expansion, loss of beneficial microbes), and disrupted metabolic pathways. AST alleviated behavioral deficits, normalized brain connectivity, and reduced the levels of proinflammatory cytokines. It also reshaped microbiota, enriching Muribaculum and Butyricicoccus, and restored metabolic profiles, increasing the levels of short-chain fatty acids and promoting bile acid pathways. Integrated analysis linked microbiota restoration to reduced neuroinflammation and improved neuroprotection.

CONCLUSION: AST modulates the gut-brain axis to counteract SD-induced dysbiosis, neuroinflammation, and metabolic imbalance, alleviating depression-like symptoms. These findings offer novel mechanistic insights into the therapeutic potential of AST for SD-related neuropsychiatric conditions.}, } @article {pmid40540838, year = {2025}, author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO}, title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.}, journal = {Microbiological research}, volume = {299}, number = {}, pages = {128260}, doi = {10.1016/j.micres.2025.128260}, pmid = {40540838}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Citrus/microbiology/growth & development ; *Organic Agriculture/methods ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Soil/chemistry ; *Agriculture/methods ; Sicily ; Biodiversity ; Plant Roots/microbiology ; Nitrogen Fixation ; }, abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.}, } @article {pmid40539808, year = {2025}, author = {Sun, H and Chen, Q and Zhang, D and Hu, L and Li, S and Lu, M and Wang, Y and Su, H and Gao, Y and Guo, J and Zhao, Y and Du, J and Liu, C and Xia, H and Xu, Y and Ge, X and Yang, Q}, title = {Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0156324}, pmid = {40539808}, issn = {2165-0497}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Microbiota ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung/microbiology ; *Mycobacterium tuberculosis/isolation & purification/genetics ; Female ; Male ; Middle Aged ; Adult ; Sensitivity and Specificity ; Sputum/microbiology ; Aged ; Young Adult ; ROC Curve ; }, abstract = {UNLABELLED: This study investigated the diagnostic potential of mNGS for detecting MTB in pulmonary tuberculosis patients. We analyzed pulmonary microbiome data to assess its impact on mNGS diagnostic accuracy and explored the association between microbiome profiles and clinical diagnosis. Bronchoalveolar lavage fluid samples were collected from 236 patients with pulmonary infections, and the diagnostic performance of mNGS was compared with traditional methods in detecting MTB. Furthermore, the incidence of false negatives and false positives, as well as the characteristics of the lung microbiota in TB patients, was analyzed to improve the diagnostic precision of mNGS. We observed that among all detection methods, mNGS showed the highest sensitivity (73.33%), followed by X-pert (60.00%), culture (53.33%), RT-PCR (53.33%), and sputum smear (23.33%). Notably, mNGS produced 3 false positive results in 236 samples, yielding a specificity of 98.54%. Analysis of the pulmonary microbiome revealed significant differences in both α-diversity and β-diversity between patients with TB and uninfected controls (P<0.05). Shannon index and Chao1 index were identified as significant predictors associated with MTB infection. ROC curve analysis demonstrated an AUC of 0.765, indicating good discriminatory performance. This study suggested that integrating wet-laboratory techniques with bioinformatics analysis can further enhance the diagnostic accuracy of mNGS for TB. Furthermore, microbiome analysis holds significant potential for the diagnosis of MTB infection.

IMPORTANCE: This study focuses on the application of next-generation sequencing (NGS) technology in detecting Mycobacterium tuberculosis in bronchoalveolar lavage fluid and explores the impact of M. tuberculosis infection on the pulmonary microbiome. By optimizing the methods and conducting microbial analyses, the accuracy of metagenomic NGS for detecting M. tuberculosis has been improved.}, } @article {pmid40539782, year = {2025}, author = {Qi, Y-H and Ye, Z-X and Feng, K-H and Ma, X-W and Zhang, C-X and Hu, M-H and Shi, M and Chen, J-P and Li, J-M}, title = {Diversity and evolutionary history of RNA viruses among different horseshoe crab species.}, journal = {Journal of virology}, volume = {99}, number = {7}, pages = {e0016425}, pmid = {40539782}, issn = {1098-5514}, support = {2022ZD03//Key Laboratory of Tropical Marine Ecosystem and Bioresource, Ministry of Natural Resources/ ; 2019B10004//Ningbo Science and Technology Innovation 2025 Major Project/ ; }, mesh = {Animals ; *Horseshoe Crabs/virology/classification ; *RNA Viruses/genetics/classification ; Phylogeny ; *Evolution, Molecular ; Genome, Viral ; Genetic Variation ; Virome ; }, abstract = {Horseshoe crabs (Xiphosura: Limulidae) are the sole surviving species of the class Merostomata, with only four extant species remaining today. Recent advances in metagenomic next-generation sequencing have unveiled a vast diversity of RNA viruses and non-retroviral endogenous RNA viral elements (nrEVEs) in invertebrates. This raises intriguing questions about the RNA virome and nrEVEs in horseshoe crabs as "living fossils," potentially offering insights into the evolutionary relationships between RNA viruses and these ancient organisms. In this study, 22 novel RNA viruses were identified across the four horseshoe crab species by screening 117 data sets, including picornaviruses, totiviruses, a flavivirus, a rhabdovirus, as well as a plant-associated tombusvirus and a fungi-associated narnavirus. Additionally, 20 nrEVEs were identified in the genomes of the four horseshoe crab species (hcEVEs), with most sharing homology with the viral family Chuviridae (N = 11), supporting the hypothesis that modern negative-sense RNA viruses may trace their origins to ancient oceanic chuviruses. A time-scaled phylogenetic tree based on hcEVEs suggests that at least two independent ancient chuvirus infections and genome integration events occurred in the common ancestor of horseshoe crab species. Interestingly, transcriptional analyses indicated that hcEVE-containing transcripts display typical exon-intron structures in the three Asian horseshoe crab species, suggesting that these hcEVEs may have been co-opted by horseshoe crabs during coevolution. These findings advance our understanding of the RNA viruses associated with horseshoe crabs and shed light on the potential role of RNA viruses in shaping the evolutionary history of this "living fossil" arthropod host.IMPORTANCERecent studies have discovered abundant RNA viruses in invertebrates, revealing that viral genomes may integrate into host genomes, creating a genetic record of past infections. In this study, we explored the evolutionary relationship between RNA viruses and the four extant horseshoe crab species-the last representatives of the class Merostomata, often termed "living fossils"-by analyzing viral sequences embedded in their genomes. The presence of chuvirus-like sequences in the genomes of these horseshoe crabs suggests that modern negative-sense RNA viruses may trace their origins back to ancient chuviruses from the ocean. Furthermore, we identified at least two independent ancient integrations of chuviruses in the evolutionary history of horseshoe crabs, with one orthologous gene containing a chuvirus-derived G protein gene/coding sequence potentially inherited from a common ancestor of the three Asian species before their divergence. Our findings contribute to a deeper understanding of the long-term coevolution between RNA viruses and their arthropod hosts.}, } @article {pmid40537892, year = {2025}, author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ}, title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2503018}, pmid = {40537892}, issn = {1738-8872}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Adolescent ; RNA, Ribosomal, 16S/genetics ; *Life Style ; Feces/microbiology ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Biodiversity ; DNA, Bacterial/genetics ; Exercise ; Sequence Analysis, DNA ; }, abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.}, } @article {pmid40537881, year = {2025}, author = {Linghu, Y and Hu, RS and Tang, XM and Li, RT and Li, WY and Wu, JH}, title = {Unveiling viral diversity and dynamics in mosquitoes through metagenomic analysis in Guizhou Province, China.}, journal = {Infectious diseases of poverty}, volume = {14}, number = {1}, pages = {51}, pmid = {40537881}, issn = {2049-9957}, support = {Qian Ke He Platform Talent-GCC [2022] 033-1//The Training Project for High-Level Innovative talents in Guizhou Province, China/ ; Qian Ke He Platform Talent-CXTD [2022] 004//The Science and Technology Innovation Talent team of Guizhou Province, China/ ; Project Contract Number: Xiao Bo He J Zi [2023] 44//The Scientific Research Foundation for Advanced Talents, Guizhou Medical University/ ; NO. 2024GCC16Z//The High-level Talent Research Start-up Project of Sichuan University of Arts and Science/ ; }, mesh = {Animals ; China ; *Mosquito Vectors/virology ; Metagenomics ; *Culicidae/virology ; *Virome ; Humans ; *Viruses/genetics/classification/isolation & purification ; Biodiversity ; }, abstract = {BACKGROUND: Poverty, disease, and vector ecology intersect to present ongoing health threats, particularly in ecologically sensitive regions. Guizhou Province in China, with its complex karst topography and rich biodiversity, offers a unique environment to study mosquito-borne viral transmission. Despite over 5000 reported cases of Japanese encephalitis in the past two decades and the detection of Zika virus in 2016, the virological landscape of this region remains poorly understood. This study aims to characterize the mosquito-associated virome, assess viral diversity, and identify factors influencing transmission dynamics in Guizhou Province.

METHODS: Between 2021 and 2022, we conducted a 2-year mosquito surveillance across eight ecologically distinct regions in Guizhou Province. Adult mosquitoes were collected using a variety of methods, including BG Mosquitaire CO2 traps, mosquito-killing lamps, manual collection, human bait traps, and oviposition traps. To investigate the virome diversity and dynamics within mosquito populations, we performed metagenomic sequencing and bioinformatics analysis on pooled mosquito samples collected from geographically diverse sampling sites.

RESULTS: We collected more than 40,000 adult mosquitoes, primarily belonging to four genera: Aedes, Anopheles, Armigeres, and Culex. Dominant species included Aedes albopictus, Anopheles sinensis, Armigeres subalbatus, and Culex tritaeniorhynchus. Notably, we report the first provincial record of the Anopheles baileyi complex, expanding the known distribution of mosquito vector in this region. Viral metagenomic sequencing, coupled with bioinformatic analysis, identified 162 viral contigs, including 140 known and 22 previously uncharacterized viruses. We experimentally confirmed the genotypes of three medically important zoonotic viruses: Japanese encephalitis virus (JEV-GI), Getah virus (GETV-GIII) and Banna virus (BAV-A2). Comparative analysis of viral abundance across mosquito species revealed that Aedes albopictus populations in Guizhou harbor a distinct virome composition, diverging from those reported in other geographic regions.

CONCLUSIONS: This study presents the comprehensive characterization of the mosquito-associated virome in Guizhou Province, providing critical insights into viral diversity, vector competence, and transmission dynamics within karst ecosystems. The detection of multiple zoonotic viruses highlights the need for strengthened surveillance and targeted public health interventions in this region.}, } @article {pmid40537448, year = {2025}, author = {Rudi, K and Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Philip, M and Martin, J and Sundt, MØ and Snipen, LG}, title = {The Coastal Seafloor Microbiota Is Structured by Local Selection of Cosmopolitan Taxa.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70123}, pmid = {40537448}, issn = {1758-2229}, support = {320076//Norges Forskningsråd/ ; }, mesh = {*Microbiota ; *Seawater/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Iceland ; Norway ; *Archaea/genetics/classification/isolation & purification/metabolism ; Metagenome ; Phylogeny ; Nitrates/metabolism ; Ecosystem ; }, abstract = {Understanding the assembly processes of the coastal seafloor microbiota is crucial for gaining insights into how ocean ecosystems work. In our study, we addressed the question about how local selection affects the global distribution of coastal seafloor microorganisms. We identified two main clusters of samples by examining the geographical distribution of 356 high-quality prokaryote metagenome-assembled genomes (MAGs) from 94 coastal samples collected along the Norwegian and Icelandic coasts. There was no identifiable correlation between the abundance of MAGs and the geographic distance between them central to the identified clusters (no distance decay). In contrast, noncentral MAGs demonstrate a pronounced distance decay. We also observed significant functional differences between the two sample clusters. One cluster showed enrichment in functions such as dissimilatory nitrate reduction to ammonium (DNRA), acetoclastic methanogenesis, thiosulphate conversion and acetate and butyrate metabolism. The other cluster was enriched in propionate metabolism, nitrite oxidation to nitrate and cobalamin-dependent carbon fixation. These results suggest that localised environmental selection acts on cosmopolitan taxa to shape seafloor microbiota. Our findings therefore profoundly impact the understanding of seafloor ecological processes and their management.}, } @article {pmid40535544, year = {2025}, author = {Wang, X and Cao, D and Chen, W and Sun, J and Hu, H}, title = {Metagenomics reveals unique gut mycobiome biomarkers in major depressive disorder - a non-invasive method.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1582522}, pmid = {40535544}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Depressive Disorder, Major/microbiology/diagnosis ; *Mycobiome ; Biomarkers/analysis ; Male ; Female ; Adult ; *Metagenomics/methods ; *Fungi/classification/genetics/isolation & purification ; Middle Aged ; Machine Learning ; Support Vector Machine ; Case-Control Studies ; Feces/microbiology ; }, abstract = {BACKGROUND: An increasing amount of evidence suggests a potential link between alterations in the intestinal microbiota and the onset of various psychiatric disorders, including depression. Nevertheless, the precise nature of the link between depression and the intestinal microbiota remains largely unknown. A significant proportion of previous research has concentrated on the study of gut bacterial communities, with relatively little attention paid to the link between gut mycobiome and depression.

METHODS: In this research, we analyzed the composition and differences of intestinal fungal communities between major depressive disorder (MDD) and healthy controls. Subsequently, we constructed a machine learning model using support vector machine-recursive feature elimination to search for potential fungal markers for MDD.

RESULTS: Our findings indicated that the composition and beta diversity of intestinal fungal communities were significantly changed in MDD compared to the healthy controls. A total of 22 specific fungal community markers were screened out by machine learning, and the predictive model had promising performance in the prediction of MDD (area under the curve, AUC = 1.000). Additionally, the intestinal fungal communities demonstrated satisfactory performance in the validation cohort, with an AUC of 0.884 (95% CI: 0.7871-0.9476) in the Russian validation cohort, which consisted of 36 patients with MDD and 36 healthy individuals. The AUC for the Wuhan validation cohort was 0.838 (95% CI: 0.7403-0.9102), which included 40 patients with MDD and 42 healthy individuals.

CONCLUSION: To summarize, our research revealed the characterization of intestinal fungal communities in MDD and developed a prediction model based on specific intestinal fungal communities. Although MDD has well-established diagnostic criteria, the strategy based on the model of gut fungal communities may offer predictive biomarkers for MDD.}, } @article {pmid40535541, year = {2025}, author = {Kato-Kogoe, N and Tsuda, K and Kudo, A and Sakaguchi, S and Omori, M and Komori, E and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Tamaki, J and Ueno, T}, title = {Salivary microbiota and IgA responses are different in pre-diabetic individuals compared to normoglycemic controls.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1591285}, pmid = {40535541}, issn = {2235-2988}, mesh = {Humans ; *Saliva/microbiology/immunology ; Female ; Male ; *Immunoglobulin A/analysis/immunology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Microbiota/immunology ; *Prediabetic State/immunology/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Diabetes Mellitus, Type 2/immunology/microbiology ; Aged ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; }, abstract = {INTRODUCTION: In recent years, changes in the oral microbiota of patients with type 2 diabetes mellitus (T2DM) have been increasingly recognized. The salivary microbiota may also be altered in pre-diabetes, which is the earliest stage of abnormal blood glucose regulation and a reversible stage preceding T2DM; however, its characteristics are poorly understood. Salivary immunoglobulin A (IgA) is a host defense factor central to the oral immune system and may play an important role in regulating the salivary microbiota. Given that alterations in immunoreactivity are observed in pre-diabetes, we hypothesized that the salivary IgA response may also be altered; however, limited knowledge exists regarding this. Therefore, in the present study, we aimed to evaluate the characteristics of salivary microbiota and IgA responses against salivary microbiota in individuals with pre-diabetes, comparing them to those in individuals with normoglycemia.

METHODS: Saliva samples were collected from 101 pre-diabetic individuals (PreDM group) and 101 age- and sex-matched normoglycemic controls (Normal group). Further, 16S rRNA metagenomic analysis was performed to compare bacterial microbiota composition. For each of the 19 saliva samples from the PreDM and Normal groups, IgA-enriched and IgA-nonenriched fractions were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. The IgA index was calculated to evaluate the difference in the IgA response to each bacterium between the PreDM and Normal groups.

RESULTS: Bacterial species richness was significantly lower in the PreDM group than in the Normal group (observed operational taxonomic unit index, p = 0.042), and a difference between these groups was noted in the overall salivary microbiota structure (unweighted UniFrac distances, p = 0.009). Salivary IgA responses against several bacterial genera differed between the PreDM and Normal groups. Significantly higher IgA responses were noted against Haemophilus in the PreDM group, with lower responses against Capnocytophaga, Corynebacterium, and Streptococcus relative to those in the Normal group.

CONCLUSIONS: Salivary microbiota and IgA responses differ between pre-diabetic individuals and normoglycemic controls. The current findings advance our understanding of the interaction between oral bacteria and host immune responses in patients with a poor glycemic status.}, } @article {pmid40533170, year = {2025}, author = {Kumari Nawarathna, TNT and Fujii, N and Yamamoto, K and Kuroda, K and Narihiro, T and Ozaki, N and Ohashi, A and Kindaichi, T}, title = {Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.}, journal = {Microbes and environments}, volume = {40}, number = {2}, pages = {}, pmid = {40533170}, issn = {1347-4405}, mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Carbon Cycle ; Metagenomics ; *Microbial Consortia/genetics ; *Ammonia/metabolism ; Folic Acid/metabolism/biosynthesis ; *Seawater/microbiology ; Metagenome ; Bioreactors/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Genome, Bacterial ; Wastewater/microbiology ; Carbon/metabolism ; }, abstract = {Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using [14]C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L[-1] of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.}, } @article {pmid40532861, year = {2025}, author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK}, title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107815}, doi = {10.1016/j.micpath.2025.107815}, pmid = {40532861}, issn = {1096-1208}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/metabolism ; Rats ; Fermentation ; Metagenomics ; Antioxidants/pharmacology/metabolism ; Molecular Docking Simulation ; Plant Extracts/metabolism/chemistry/pharmacology ; Terminalia/metabolism/chemistry ; Male ; Rats, Wistar ; Anti-Bacterial Agents/pharmacology/metabolism ; Liver/drug effects/pathology ; *Lactobacillus plantarum/metabolism ; Gallic Acid/metabolism ; Kidney/drug effects/pathology ; Spleen/drug effects/pathology ; }, abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.}, } @article {pmid40532815, year = {2025}, author = {Pan, D and Sun, H and Liu, Y and Wang, J and Kuang, Y and Shi, T and Zhang, H}, title = {Mobilome dominates fomesafen-responsive dissemination of antibiotic resistome in manure-amended agricultural soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126686}, doi = {10.1016/j.envpol.2025.126686}, pmid = {40532815}, issn = {1873-6424}, mesh = {Manure ; *Soil Microbiology ; Agriculture ; *Herbicides ; Soil/chemistry ; *Soil Pollutants ; *Drug Resistance, Microbial/genetics ; *Benzamides ; Microbiota ; }, abstract = {Pesticides are increasingly perceived as emerging drivers in the spread of antibiotic resistance genes (ARGs) within agroecosystems. Pesticides with longer half-lives tend to impose persistent stresses on soil microbiomes, yet the selection for ARG dissemination remains overlooked. Focusing on a widely used long residual herbicide fomesafen, we examined recommended dose-based selection on the dissemination of ARGs in agricultural soils with or without manure amendment. The degradation half-lives of fomesafen in the blank soils and manure-amended soils were 35.77-124.00 and 20.00-73.27 d, respectively. After 42-d exposure, the total abundances of ARGs in the fomesafen-treated manure-amended soils at exposure concentrations of 1 and 5 mg/kg were 1.20- and 1.36-fold higher than that in the controls, with the changes of mobile genetic elements (MGEs) reaching 1.24-2.22 folds; while no significant change was observed in the blank soils. Furthermore, no significant change was observed in either bacterial communities or ARG-carrying metagenome-assembled genomes in both manure-amended soils and blank soils under fomesafen selection. Variation partition analysis suggested that 24.42%-25.41% of the variations in ARGs could be individually explained by MGEs, while only 13.47%-13.75% by bacterial communities. Overall, these findings demonstrate that MGE-mediated horizontal transfer predominates fomesafen-responsive dissemination of ARGs in manure-amended agriculture soils and underscores the urgency of re-evaluating agricultural practices involving co-application of manures and long residual herbicides.}, } @article {pmid40532696, year = {2025}, author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and , and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL}, title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.}, journal = {Cell}, volume = {188}, number = {16}, pages = {4257-4274.e13}, pmid = {40532696}, issn = {1097-4172}, support = {Z01 HG000180/ImNIH/Intramural NIH HHS/United States ; ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; R01 AI183416/AI/NIAID NIH HHS/United States ; Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; ZIA AI001255/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota ; *Trichophyton/drug effects/isolation & purification/genetics ; Malaysia/epidemiology ; Male ; Female ; *Tinea/microbiology/epidemiology ; Adult ; Antifungal Agents/pharmacology/therapeutic use ; Middle Aged ; Terbinafine/pharmacology ; Young Adult ; Drug Resistance, Fungal ; Southeast Asian People ; }, abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.}, } @article {pmid40532529, year = {2025}, author = {Parab, AS and Ghose, M and Manohar, CS}, title = {Metagenomic reconstruction of microbial genomes and biogeochemical pathways: insights into carbon and nitrogen flux dynamics in the eastern Arabian Sea.}, journal = {Marine environmental research}, volume = {210}, number = {}, pages = {107292}, doi = {10.1016/j.marenvres.2025.107292}, pmid = {40532529}, issn = {1879-0291}, mesh = {Nitrogen/metabolism/analysis ; Seawater/microbiology/chemistry ; *Nitrogen Cycle ; Metagenomics ; Carbon/metabolism ; *Metagenome ; Bacteria/genetics ; *Carbon Cycle ; *Genome, Microbial ; Seasons ; Microbiota ; }, abstract = {The eastern Arabian Sea (EAS) experiences seasonal nutrient availability and productivity shifts driven by the Indian monsoon, influencing microbial contributions to biogeochemical cycles. This study explores carbon, nitrogen and sulfur cycling using metagenome-assembled genomes (MAGs) from water samples collected at chlorophyll maxima (C-Max) depths during non-monsoon and monsoon seasons. A total of 49 high-quality MAGs were reconstructed from 12 metagenomic samples, including four novel lineages from the phyla Pseudomonadota and Bacteroidota. These MAGs revealed distinct seasonal shifts in microbial composition and function. During the non-monsoon season, microbial communities dominated by Idiomarina and Marinobacter showed increased gene abundance for C1 compound metabolism, nitrogen cycling and sulfur oxidation, processes essential for managing climate-active gases such as carbon dioxide (CO2) and nitrous oxide (N2O), while also preventing toxic sulfide accumulation. In contrast, monsoon conditions enhanced organic matter influx, promoting nitrogen retention pathways driven by Sinimarinibacterium and Oleibacter, raising concerns about potential nutrient buildup and localized hypoxia. Despite seasonal variations, functional redundancy ensured the stability of nutrient cycling processes. PERMANOVA analysis (p < 0.001) confirmed that microbial functional gene distribution was primarily shaped by taxonomic structure, with genus-level composition playing a dominant role. The study highlights microbial adaptability and resilience, ensuring ecosystem stability in the dynamic EAS environment. Understanding microbial processes at C-Max depths has enhanced our understanding of biogeochemical cycling in the EAS. Although focused on oxygenated depths, these findings offer insights relevant to microbial functions in the OMZ, reflecting the distinct environmental conditions of EASs.}, } @article {pmid40530883, year = {2025}, author = {Ganote, CL and Caesar, L and Rice, DW and Whitaker, RJ and Newton, ILG}, title = {Evolutionary trends in Bombella apis CRISPR-Cas systems.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0016625}, pmid = {40530883}, issn = {2379-5077}, support = {2005306//National Science Foundation/ ; }, mesh = {*CRISPR-Cas Systems/genetics ; Animals ; Bees/microbiology/genetics ; *Evolution, Molecular ; Gastrointestinal Microbiome ; Phylogeny ; }, abstract = {UNLABELLED: Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis. B. apis is an important honey bee symbiont, found primarily in larvae, queens, and hive compartments. B. apis is found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.

IMPORTANCE: Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen's digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.}, } @article {pmid40530822, year = {2025}, author = {Wu, H and Sun, B and Li, J}, title = {Metagenomics research on PAH biodegradation in the lower reaches of the Shiwuli River in Chaohu, China.}, journal = {Environmental science. Processes & impacts}, volume = {27}, number = {7}, pages = {2188-2197}, doi = {10.1039/d5em00025d}, pmid = {40530822}, issn = {2050-7895}, mesh = {Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism/analysis ; China ; Metagenomics ; *Water Pollutants, Chemical/metabolism/analysis ; *Rivers/microbiology/chemistry ; Bacteria/metabolism ; }, abstract = {Metagenomics is a powerful tool for investigating functional microorganisms, molecular mechanisms and genes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) in situ complex environments. In this study, we selected three land use types in the lower reaches of the Shiwuli River in Chaohu and applied metagenomics technology. The results revealed that Rhodoplanes and Bradyrhizobium were the abundant PAH-degrading microorganisms across the three land use types. Based on the functional annotation and PAH degradation pathway, it was found that the in situ microbial communities of the three land use types shared common metabolic pathways for phenanthrene degradation. In addition, a unique metabolic pathway for PAH degradation was identified in the agricultural land. Only Patulibacter contributed to flnE (KO14604) in the agricultural land, which was involved in the metabolic pathway of fluorene degradation. Results of this study suggested that the in situ degradation of PAHs was not completed by a single genus, and it involved the synergy effects of different PAH-degrading microorganisms. There was no significant difference between the compositions and relative abundances of PAH-degrading microorganisms in the three land use types and those presented in the Kyoto Encyclopedia of Genes and Genomes Orthology (KO). However, the same microorganism contributed to different functional genes in different samples. Genes encoding protocatechuic acid 4,5-dioxygenase were widely distributed and relatively abundant. Therefore, this gene may serve as an indicator of PAH degradation potential. Among all the factors, the total organic carbon and nitrate nitrogen contents exhibited significant influences on the functional genes (KO) related to PAH degradation (p < 0.05).}, } @article {pmid40528698, year = {2025}, author = {Bonilla-Espadas, M and Lifante-Martínez, I and Camacho, M and Orgilés-Calpena, E and Arán-Aís, F and Bertazzo, M and Bonete, MJ}, title = {Chromium-Tanned Leather and Microbial Consortia: Identification of Taxa With Biodegradation Potential and Chromium Tolerance.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70134}, pmid = {40528698}, issn = {1758-2229}, support = {IMDEEA/2021/11//European Union through the European Regional Development Fund within the Operational Programme of the Valencian Community 2014-2020/ ; UAIND21-02B//Universidad de Alicante/ ; }, mesh = {*Chromium/metabolism/toxicity ; *Microbial Consortia ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Microscopy, Electron, Scanning ; Tanning ; }, abstract = {Chromium-tanned leather waste poses significant environmental challenges due to its resistance to degradation and heavy metal content. This study investigates the potential of naturally selected microbial consortia to initiate the degradation of chromium-tanned leather and identifies key bacterial genera capable of tolerating chromium and producing enzymes relevant to collagen breakdown. A novel multidisciplinary approach combining gravimetric assays, metagenomic sequencing, and scanning electron microscopy (SEM) was applied to characterise both microbial composition and degradation dynamics. Dominant genera such as Bacillus, Microbacterium, and Acinetobacter were associated with collagen degradation and metal tolerance, with Bacillus-rich communities showing the most pronounced mass loss (up to 3%). SEM analysis revealed the formation of robust biofilms and extensive matrix disruption, indicating enzymatic activity and structural breakdown of the leather. The formation of exopolysaccharide-rich biofilms was found to be critical for microbial adhesion and biodegradation efficacy. These findings provide initial insights into microbial mechanisms involved in the degradation of chromium-tanned leather and suggest potential applications for microbial consortia in future sustainable leather waste management strategies.}, } @article {pmid40528221, year = {2025}, author = {Gao, L and Liao, H and Chen, Y and Ye, C and Huang, L and Xu, M and Du, J and Zhang, J and Huang, D and Cai, S and Dong, H}, title = {Airway microbiota associated D-phenylalanine promotes non-small cell lung cancer metastasis through epithelial mesenchymal transition.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {673}, pmid = {40528221}, issn = {1479-5876}, support = {82170032//National Natural Science Foundation of China/ ; 82470058//National Natural Science Foundation of China/ ; 82270024//National Natural Science Foundation of China/ ; YZ2022ZX04//President Foundation of The Fifth Affiliated Hospital, Southern Medical University/ ; 2023A1515110216//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023M731546//China Postdoctoral Science Foundation/ ; }, mesh = {*Epithelial-Mesenchymal Transition/drug effects ; Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/microbiology ; *Lung Neoplasms/pathology/microbiology ; Animals ; Male ; Neoplasm Metastasis ; Female ; *Microbiota ; *Phenylalanine/metabolism/pharmacology/administration & dosage ; Middle Aged ; Bronchoalveolar Lavage Fluid/chemistry ; Cell Line, Tumor ; Mice ; Aged ; *Respiratory System/microbiology ; }, abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related death worldwide, and patients with distant metastasis have a poor prognosis. Various studies have reported that microbiota and metabolites significantly differ between healthy individuals and lung cancer patients. However, the effects of metabolites on tumor formation and metastasis are unclear. Therefore, our study aimed to determine the correlation between airway metabolites and microbiota, along with their respective roles in lung cancer metastasis.

METHODS: Bronchoalveolar lavage fluid (BALF) samples were collected from 30 non-small cell lung cancer (NSCLC) patients, including 11 patients without metastasis (M0) and 19 patients with metastasis (M1). Integrated pathogenic metagenomic and Liquid chromatography-mass spectrometry (LC‒MS) analyses were employed to explore differences between two groups. The omics data were analyzed and integrated via Spearman's correlation coefficient. Specific metabolites were subsequently used to intervene in lung cancer cells and animal models to assess their influence on tumor metastasis.

RESULTS: A total of 801 metabolites were identified in the BALF of all patients. Compared with those in the M0 group, 48 metabolites in the M1 group were significantly different. D-phenylalanine was notably upregulated in M1 and was positively related to Metamycoplasma salivarium. Intranasal administration of D-phenylalanine promoted tumor intrapulmonary metastasis and induced epithelial mesenchymal transition (EMT) process in NSCLC mouse models. Moreover, D-phenylalanine promotes the proliferation of non-small cell lung cancer cells and facilitates their migration and invasion via EMT.

CONCLUSION: The airway microbiota associated D-phenylalanine could promote lung cancer metastasis via EMT, which could be a new predictor for the diagnosis of tumor metastasis in NSCLC patients.}, } @article {pmid40528214, year = {2025}, author = {Zhang, Y and Luo, J and Chen, K and Li, N and Luo, C and Di, S and Qin, J and Zhang, F and Chen, H and Dai, M}, title = {Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {676}, pmid = {40528214}, issn = {1479-5876}, support = {2022-I2M-1-0031//Institute of Chinese Materia Medica, China Academy of Chinese Medical Science/ ; 82173606//National Natural Science Foundation of China/ ; 82273726//National Natural Science Foundation of China/ ; 20230484397//Beijing Nova Program of Science and Technology/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Risk Factors ; Risk Assessment ; Reproducibility of Results ; Male ; Female ; Middle Aged ; Metagenomics ; Case-Control Studies ; }, abstract = {BACKGROUND: Microbiome-wide association studies showed links between colorectal cancer (CRC) and gut microbiota. However, the clinical application of gut microbiota in CRC prevention has been hindered by the diversity of study populations and technical variations. We aimed to determine CRC-related gut microbial signatures based on cross-regional, cross-population, and cross-cohort metagenomic datasets, and elucidate its application value in CRC risk assessment.

METHODS: We used the MMUPHin tool to perform a meta-analysis of our own cohort and seven publicly available metagenomics datasets to identify gut microbial species associated with CRC across different cohorts, comprising of 570 CRC cases and 557 controls. Based on differential species sets, we constructed the microbial risk score (MRS) using α-diversity of the sub-community (MRSα), weighted/unweighted summation methods and machine learning algorithms. Cohort-to-cohort training and validation were performed to demonstrate the transferability.

RESULTS: We found that MRSα of core species was better validated and more interpretable than those constructed with summation methods or machine learning algorithms. Six species, including Parvimonas micra, Clostridium symbiosum, Peptostreptococcus stomatis, Bacteroides fragilis, Gemella morbillorum, and Fusobacterium nucleatum, were included in MRSα constructed by half or more of the cohorts. The AUC of MRSα, calculated based on the sub-community of six species, varied between 0.619 and 0.824 across the eight cohorts.

CONCLUSION: We identified six CRC-related species across regions, populations, and cohorts. The constructed MRSα could contribute to the risk prediction of CRC in different populations.}, } @article {pmid40525868, year = {2025}, author = {Wang, H and Xue, W and Cheng, J and He, Y and Song, Y and Hu, D and Peng, A and Li, C and Bao, H}, title = {Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.}, journal = {Microbiology spectrum}, volume = {13}, number = {8}, pages = {e0316624}, pmid = {40525868}, issn = {2165-0497}, support = {81692938//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Anemia/microbiology/metabolism/etiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; *Kidney Failure, Chronic/complications/microbiology/metabolism ; *Metabolome ; Metabolomics ; Metagenomics ; Prevotella ; }, abstract = {The gut microbiomes communicate with the kidney and may play a crucial role in the development of anemia in patients with chronic renal failure (CRF). However, the alterations in microbiota and their association with functional metabolites remain unclear. We performed metagenomics and untargeted metabolomics in a cohort of 30 patients with anemia of CRF and 20 healthy controls (HCs) to identify the characteristics of the gut microbiome and explore its potential interactions with the host. Decreased microbiota diversity and significant compositional differences were observed in the patients with anemia of CRF. We identified six gut microbiotas significantly changed in the patients with anemia of CRF, particularly Faecalibacterium prausnitzii, Prevotella copri, and Escherichia coli, which were closely correlated with hemoglobin (Hb) levels and estimated glomerular filtration rate (eGFR). These changes were accompanied by functional alterations in distinctive microbial pathways. Further fecal and serum metabolomics revealed fecal 12-KETE-LTB4 in arachidonic acid metabolism, uracil and L-aspartic acid in beta-alanine metabolism, gulonic acid in ascorbate and aldarate metabolism, accompanied by the top 15 differential serum metabolites that were closely correlated with Hb levels. Furthermore, we observed a complex co-occurrence between anemia of CRF-related gut microbiota species and the characterized metabolites. Moreover, a non-invasive model incorporating Faecalibacterium prausnitzii and Prevotella copri, combined with fecal 12-KETE-LTB4, uracil, L-aspartic acid, and gulonic acid, distinguished the patients with anemia of CRF from HCs (area under the curve: 0.879). Collectively, our results suggest that a disordered gut microbiome associated with functional metabolites may be a non-invasive diagnostic and therapeutic target for anemia of CRF.IMPORTANCEAnemia is a prevalent complication in patients with chronic renal failure (CRF), which is associated with a high burden of morbidity and adverse clinical outcomes. Various evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of anemia in CRF, although the mechanism is still obscure. This work provides substantial evidence identifying the specific characteristics of the gut microbiomes accompanied by functional alterations in anemia of CRF. We highlight the intricate interactions among the anemia of CRF-related gut microbiome and the functional metabolites, which may regulate toxic accumulation, oxidative stress, and immune-inflammatory responses to induce and exacerbate anemia in patients with CRF. Furthermore, we found that evaluating the gut microbiota and fecal metabolites in combination might be a non-invasive prognostic indicator of CRF-induced anemia. These findings provide important insights into the role of gut microbiota in the mechanism of anemia in CRF.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05543291.}, } @article {pmid40523923, year = {2025}, author = {Zhang, M and Liang, C and Li, B and Jiang, F and Song, P and Gu, H and Gao, H and Cai, Z and Zhang, T}, title = {Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {930}, pmid = {40523923}, issn = {2399-3642}, mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; *Diet/veterinary ; Sheep/microbiology ; Ecosystem ; Herbivory ; }, abstract = {The gut microbiota plays a critical role in plant digestion, nutrient absorption, and ecological adaptation in herbivores. However, how gut microbiota and diet jointly influence ecological niche differentiation in sympatric species remains unclear. Here, we use metagenomic sequencing and plant trnL (UAA) fragment sequencing to examine the gut microbiota and dietary composition of sympatric Tibetan argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) in the Kunlun Mountains of the Qinghai-Tibet Plateau. Despite inhabiting similar environments, the two species harbor distinct microbial compositions and functional profiles. Interestingly, higher dietary diversity does not correspond to higher microbial diversity. Tibetan argali, despite having a simpler diet, possesses a more diverse and flexible gut microbiome. In contrast, blue sheep show broader dietary preferences and stronger microbial metabolic adaptation to glycan biosynthesis and metabolism. These findings reveal significant associations between gut microbiota composition, function, and diet, supporting a microbial contribution to trophic niche differentiation. Our results highlight distinct microbial-dietary strategies in sympatric herbivores and underscore the role of the gut microbiome in ecological adaptation and species coexistence.}, } @article {pmid40523415, year = {2025}, author = {Xu, Y and Ontita, NC and Zeng, W and Huang, J and Jiang, L and Huang, X and Li, Q and Hu, P}, title = {High-efficiency nitrogen removal by cold-tolerant bacteria consortium at low temperatures.}, journal = {Bioresource technology}, volume = {434}, number = {}, pages = {132816}, doi = {10.1016/j.biortech.2025.132816}, pmid = {40523415}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Cold Temperature ; Wastewater/chemistry ; *Bacteria/metabolism/genetics ; *Microbial Consortia/physiology ; Water Purification/methods ; }, abstract = {A cold-tolerant bacteria consortium (M2) was developed to enhance nitrogen removal efficiency in wastewater treatment processes operating at low temperatures (below 15 ℃). Bacteria consortium M2 demonstrated high removal efficiencies for nitrogen (NH4[+]-N, 97.34 %; NO3[-]-N, 97.13 %; NO2[-]-N, 59.92 %). Dominated by genera including Comamonas, Pseudomonas, and Acinetobacter, M2 produced substantial extracellular polymeric substances (EPS) and unsaturated fatty acids, which mitigated cold-induced stress. Metagenomic analysis revealed the presence of cold-shock responsive genes, including unsaturated fatty acid synthase, and cpsA, which contribute to its resilience under low-temperature conditions. Moreover, M2 enhanced both nitrogen assimilation and nitrate reduction under cold stress. These findings highlight the potential of M2 as an effective and practical strategy for improving nitrogen removal in wastewater treatment facilities during winter, thereby addressing a critical operational limitation in cold-climate regions.}, } @article {pmid40523310, year = {2025}, author = {Johnson, L and Smith, D and Subasinghe, R and Raap, M and Richter, R and Huyben, D and Lau, C and Brown, L and Chu, J and Khomenko, O and Manning, A and Johnson, S and Hamoutene, D}, title = {Influence of aquaculture and genomic surveillance techniques on antimicrobial resistance gene profiles and microbiota detected in marine and freshwater sediments.}, journal = {Canadian journal of microbiology}, volume = {71}, number = {}, pages = {1-18}, doi = {10.1139/cjm-2024-0206}, pmid = {40523310}, issn = {1480-3275}, mesh = {*Geologic Sediments/microbiology ; *Aquaculture ; *Fresh Water/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Seawater/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Animals ; *Drug Resistance, Bacterial/genetics ; Canada ; }, abstract = {Surveillance methods for antimicrobial resistance genes (ARGs) are needed to assess potential risk of antimicrobial resistance, especially in complex environmental samples with limited data on ARG distribution. This study employed target-enrichment metagenomics (bait-capture) and a Resistomap qPCR assay to assess the resistome in marine and freshwater sediments associated with active Canadian finfish aquaculture operations. Differences in resistome profiles were considered with distance to the net-pens, concentrations of three aquaculture-associated chemical residues, and microbial communities as detected with 16S rRNA gene amplicon sequencing. With bait-capture, a total of 194 ARGs and 41 replicon types were detected across the sediment samples. Differences due to aquaculture proximity were noted in the composition of the resistome, which was dominated by tetracycline resistance genes. With qPCR, 37 out of 51 ARGs targets were detected, and proximity to net-pens or region did not show changes in resistome composition. Co-occurrence networks revealed significant correlations among genera and the resistome detected with bait-capture, highlighting a potential influence of aquaculture on ARGs in the environment. This study demonstrates the utility of bait-capture and qPCR assays in detection of ARGs in both freshwater and marine sediments from aquaculture sites that will assist further ARG surveillance.}, } @article {pmid40520638, year = {2025}, author = {Zakaria, D and Sandri, C and Modesto, M and Spiezio, C and Scarafile, D and Cedras, A and Borruso, L and Manghi, P and Trevisi, P and Segata, N and Mattarelli, P and Arita, M}, title = {Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19566}, pmid = {40520638}, issn = {2167-8359}, mesh = {Animals ; *Turtles/microbiology ; *Gastrointestinal Microbiome/genetics ; Italy ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Age Factors ; Seychelles ; Environment ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The gut microbiota plays a pivotal role in regulating the physiological functions of its host, including immunity, metabolism, and digestion. The impact of environment and age on microbiota can be assessed by observing long-lived animals across different age groups and environments. The Aldabra giant tortoise (Aldabrachelys gigantea) is an ideal species for this study due to its exceptionally long lifespan of over 100 years.

METHODS: Using 16S rRNA gene amplicon analysis, we analyzed 52 fecal samples from giant tortoises in Seychelles (Curieuse and Mahé islands) and in a zoological park in Italy, from very young individuals to those of >100 years old. We performed Alpha and Beta diversity analysis, relative abundance analysis, and complex upset plot analysis, comparing the results of tortoises from different environments and age groups.

RESULTS: The diversity and overall composition of the gut microbiota of tortoises were impacted mainly by geolocation rather than their age. The greater diversity of microbiota in wild tortoises was attributed to their food variance such as wild leaves and branches, compared to captive or domesticated conditions. Beta diversity analysis also revealed the contribution of both environment and age to the variation between samples, with environments accounting for a larger proportion of this contribution. Certain bacterial families, such as Spirochaetota and Fibrobacterota, were more prevalent in environments with higher fiber intake, reflecting dietary differences. Additionally, a range of host-independent environmental bacteria was found to be specific to individuals in Curieuse and not in other geolocations. On the other hand, there were no bacterial taxa specific to centenarians, whose microbial complexity was reduced compared to adult or elderly tortoises.

CONCLUSIONS: Our records showed that environment is the primary influence in the overall composition and diversity of the gut microbiota of Aldabra giant tortoises. As giant tortoises are amongst the longest-lived vertebrate animals, these findings can be utilized to monitor their health according to their ages, and enhance their conservation efforts.}, } @article {pmid40520307, year = {2025}, author = {Ye, S and Peng, S and Wang, X and Fan, J and Zhu, C and Huang, L and Huang, Y and Cheng, K and Ni, T and Qian, Y and Wu, X and Xu, Y}, title = {Microbial community structure and resistome dynamics on elevator buttons in response to surface disinfection practices.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1593114}, pmid = {40520307}, issn = {2296-2565}, mesh = {*Disinfection/methods ; *Disinfectants/pharmacology ; Humans ; COVID-19/prevention & control ; China ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Microbiota/drug effects ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Disinfectants have been extensively used in public environments since the COVID-19 outbreak to help control the spread of the virus. This study aims to investigate whether disinfectant use influences the structure of bacterial communities and contributes to bacterial resistance to disinfectants and antibiotics.

METHODS: Using molecular biology techniques-including metagenomic sequencing and quantitative PCR (qPCR)-we analyzed the bacterial communities on elevator button surfaces from two tertiary hospitals, one infectious disease hospital, two quarantine hotels (designated for COVID-19 control), and five general hotels in Nanjing, Jiangsu Province, during the COVID-19 pandemic. We focused on detecting disinfectant resistance genes (DRGs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs).

RESULTS: Significant differences were observed in the bacterial community structures on elevator button surfaces across the four types of environments. Quarantine hotels, which implemented the most frequent disinfection protocols, exhibited distinct bacterial profiles at the phylum, genus, and species levels. Both α-diversity (within-sample diversity) and β-diversity (between-sample diversity) were lower and more distinct in quarantine hotels compared to the other environments. The abundance of DRGs, ARGs, and MGEs was also significantly higher on elevator button surfaces in quarantine hotels. Notably, antibiotic-resistant bacteria (ARBs), including Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa, were detected in all four settings.

CONCLUSION: The structure of bacterial communities on elevator button surfaces varies across different environments, likely influenced by the frequency of disinfectant use. Increased resistance gene abundance in quarantine hotels suggests that disinfection practices may contribute to the selection and spread of resistant bacteria. Enhanced monitoring of disinfection effectiveness and refinement of protocols in high-risk environments such as hospitals and hotels are essential to limit the spread of resistant pathogens.}, } @article {pmid40517714, year = {2025}, author = {Huang, H and Xiao, K and Shen, T and Chu, D and Xie, Z and Bi, Y and Ning, K and Yan, Y}, title = {The impact of enclosure management on the conservation and restoration of microbial community in a typical urban lake.}, journal = {The Science of the total environment}, volume = {989}, number = {}, pages = {179827}, doi = {10.1016/j.scitotenv.2025.179827}, pmid = {40517714}, issn = {1879-1026}, mesh = {*Lakes/microbiology ; *Microbiota ; *Conservation of Natural Resources/methods ; *Environmental Restoration and Remediation/methods ; China ; Ecosystem ; *Environmental Monitoring ; *Water Microbiology ; }, abstract = {Urban lake freshwater ecosystems, as vital lifelines intricately connected to human well-being, hosted microbes vital for biosynthetic and global biochemical cycles. Despite their ecological importance, current research has yet to fully elucidate how urban lake restoration efforts influence microbial diversity, community structure, and functional dynamics, leaving a significant gap in our understanding of the ecological outcomes of such interventions. Donghu Lake's ongoing restoration project employs enclosure management as a conservation strategy. To evaluate the impact of enclosure management on protecting and restoring microbial communities, we analyzed 72 metagenomic samples from the restoration waterbody. It was found that enclosure management profoundly reshaped microbial communities, making them more stable and similar to natural conditions, and boosting their biosynthetic gene encoding potential. Furthermore, research revealed antibiotic resistance genes (ARGs) tended to be preferentially hosted by specific microbes, identifying Gammaproteobacteria as a critical target for managing ARGs proliferation. These findings provide not only a fresh perspective for the understanding, but also a robust foundation for the management of urban lake freshwater ecosystems. Our findings highlight that enclosure management promotes microbial community stability and functional resilience, which are critical for restoring ecosystem services in urban lakes. This study provides actionable insights for designing targeted conservation strategies to enhance the sustainability of freshwater ecosystems under anthropogenic pressure.}, } @article {pmid40517504, year = {2025}, author = {Tang, X and Liu, Y and Yang, W and Wu, Y and Yong, T and Liu, W and Lv, F and Hussain, K and Wang, Y and Gao, X and Zhang, Y}, title = {Macroplastics in soybean cultivation: Neutral on plant growth but disruptive to nitrogen-fixing microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {301}, number = {}, pages = {118499}, doi = {10.1016/j.ecoenv.2025.118499}, pmid = {40517504}, issn = {1090-2414}, mesh = {*Glycine max/growth & development/drug effects/microbiology ; *Nitrogen Fixation/drug effects ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil Pollutants/toxicity ; Soil/chemistry ; Nitrogen/metabolism ; Nitrates/analysis/metabolism ; Agriculture ; Bradyrhizobium/drug effects ; Nitrogen Cycle/drug effects ; }, abstract = {Macroplastics are an emerging yet underexplored pollutant in agricultural soils, with the potential to disrupt nitrogen (N) cycling through physical interference and microbial community shifts. While extensive studies have focused on microplastics, the effects of larger plastic debris (>2 cm) on soil-plant systems in legume cropping systems remain poorly understood. We conducted a 71-d mesocosm study utilizing [15]N isotopic tracing and metagenomic sequencing to demonstrate how macroplastics influence soybean growth and soil-soybean continuum N cycling. Soybean growth was not affected under macroplastics exposure (up to 200 kg ha[-][1]). However, macroplastics increased soil NO3[-] and NH4[+] concentrations, and elevated urease and ammonia monooxygenase activities, suggesting enhanced N availability. Paradoxically, macroplastics significantly disrupted the N-fixing microbial community, reducing the abundance of key bacteria such as Azorhizobium and Bradyrhizobium. Nitrogen fixation pathways (in log10-transformed TPM+1) were markedly suppressed in soils treated with 200 kg ha[-1] macroplastics compared to untreated soils (p < 0.001). Our findings highlight the potential risks of macroplastics posing to N cycling and microbial health in agricultural soils. This study addresses a critical knowledge gap by shifting the focus from micro- to macroplastic impacts on biogeochemical cycling.}, } @article {pmid40517085, year = {2025}, author = {Schoenle, A and Francis, O and Archibald, JM and Burki, F and de Vries, J and Dumack, K and Eme, L and Florent, I and Hehenberger, E and Hoffmeyer, TT and Irisarri, I and Lara, E and Leger, MM and Lukeš, J and Massana, R and Mathur, V and Nitsche, F and Strassert, JFH and Worden, AZ and Yurchenko, V and Del Campo, J and Waldvogel, AM}, title = {Protist genomics: key to understanding eukaryotic evolution.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2025.05.004}, pmid = {40517085}, issn = {0168-9525}, abstract = {All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution. However, these mainly unicellular, microscopic organisms are understudied and the generation of protist genomes lags far behind most multicellular lineages. Current genomic methods, which are primarily designed for animals and plants, are poorly suited for protists. Advancing protist genome research requires reevaluating plant- and animal-centric genomic standards. Future efforts must leverage emerging technologies and bioinformatics tools, ultimately enhancing our understanding of eukaryotic molecular and cell biology, ecology, and evolution.}, } @article {pmid40516682, year = {2025}, author = {Sadah Al Azzawi, DH and Jalali, A and Rezaei, M}, title = {Metagenomic insights into bacterial communities and antibiotic resistance genes in landfill-impacted waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126663}, doi = {10.1016/j.envpol.2025.126663}, pmid = {40516682}, issn = {1873-6424}, mesh = {*Waste Disposal Facilities ; *Bacteria/genetics/classification ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Metagenomics ; Iran ; Environmental Monitoring ; Genes, Bacterial ; *Water Microbiology ; Microbiota ; }, abstract = {Municipal landfills are significant sources of environmental and microbial pollution, impacting groundwater and surface water quality. This study investigated the microbial community composition and antibiotic resistance genes (ARGs) in water downstream of landfills of Gilan, Mazandaran, and Golestan provinces, Iran. Water samples were collected from seven sites, and shotgun metagenomic sequencing was used to analyze microbial diversity and ARGs. Heavy metals and BTEX (benzene, toluene, ethylbenzene, and xylene) compounds were measured using inductively coupled plasma (ICP), and gas chromatography-mass spectrometry (GC-MS) methods, respectively. Pseudomonadaceae and Enterobacteriaceae were the most abundant bacterial families, with efflux pump ARGs being the most prevalent. Concentrations of arsenic and cadmium exceeded WHO and US-EPA standards at all sites. Significant positive correlations were observed between Pseudomonadaceae abundance and lead concentration (r = 0.998, p = 0.031, CI [0.966, 0.999]), and between Enterobacteriaceae abundance and chromium concentration (r = 0.999, p = 0.0078, CI [0.993, 1.000]). A significant negative correlation was found between the abundance of the two-component system (TCS) gene class and BTEX concentration (r = -0.457, p = 0.014, CI [-0.72, -0.09]). Additionally, aluminum concentration negatively correlated with antibiotic inactivation (r = 0.999, p = 0.018, CI [-1.000, -0.997]) and antibiotic target protection classes (r = -0.997, p = 0.048, CI [-0.999, -0.990]). These findings indicate that landfill sites significantly influence bacterial communities, promoting resistance to heavy metals and pollutants. The abundance of ARGs near landfills suggests microbial adaptation to pollution, highlighting the need for improved waste management to mitigate the spread of antibiotic resistance.}, } @article {pmid40516324, year = {2025}, author = {Xu, R and Li, T and Wang, Z and Wang, H and Sun, M and Xie, J and Tong, L and Peng, W and Wang, Y}, title = {Association among lean mass, gut microbiome alterations and bone mineral density in high-altitude.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {51}, number = {}, pages = {18-27}, doi = {10.1016/j.clnu.2025.05.018}, pmid = {40516324}, issn = {1532-1983}, mesh = {Humans ; *Bone Density/physiology ; *Altitude ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; Absorptiometry, Photon ; Adult ; *Body Composition/physiology ; Body Mass Index ; Tibet ; Feces/microbiology ; Lumbar Vertebrae ; }, abstract = {BACKGROUND: Body composition, particularly lean body mass, plays a pivotal role in skeletal health and has been increasingly linked to the gut microbiota (GM). However, evidence from vulnerable high-altitude populations remains scarce.

OBJECTIVE: This study aimed to evaluate the association between body composition and bone mineral density (BMD) at high altitudes and explore the potential role of GM.

METHODS: A total of 820 Tibetan participants were recruited. BMD at the lumbar spine (L1-L4) and total hip was measured using dual-energy X-ray absorptiometry (DXA). Multivariate linear regression was applied to evaluate the associations between body composition indices and BMD. Participants were stratified into low lean mass index (LLMI) and high lean mass index (HLMI) subgroups using restricted cubic splines (RCS) and body mass index. Stool samples from a subset of participants (n = 383) were analyzed to determine the relative abundances of KEGG Orthology groups.

RESULTS: LMI was positively associated with hip BMD at high altitude [β (95 % CI) = 0.005 (0.003,0.007), P < 0.05], whereas no significant association was observed with spine BMD. This correlation varied significantly by altitude (Pinter< 0.05). A similar positive relationship was observed between microbial diversity (Shannon index) and hip_BMD [hip: β (95 % CI) = 0.605 (0.165, 1.044), P < 0.05]. Compared to the HLMI group, LLMI participants exhibited greater microbial diversity (P < 0.05), higher Faecalibacteriums abundance, and lower levels of Prevotella copri (P< 0.05). Functional metagenomic analysis identified differential enrichment of microbial pathways, including riboflavin metabolism, terpenoid backbone biosynthesis, alanine, aspartate, and glutamate metabolism (P < 0.05).

CONCLUSION: These findings highlight the correlation between LMI and hip BMD among high-altitude Tibetan adults, offering a potential mechanism for the interplay between GM profiles and bone health in high-altitude populations.}, } @article {pmid40515809, year = {2025}, author = {Zhang, Z and Yang, Z and Lin, S and Jiang, S and Zhou, X and Li, J and Lu, W and Zhang, J}, title = {Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2520407}, pmid = {40515809}, issn = {1949-0984}, mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Blood Glucose/analysis/metabolism ; Adult ; Middle Aged ; Metagenomics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; }, abstract = {The gut microbiome is essential for maintaining host health, influencing gut function and metabolic regulation. While probiotics are widely used to manage gut health, evidence of their specific effects in healthy individuals remains limited. Most studies focus on diseased populations, with little attention to early interventions in individuals without major diseases. In this study, we investigated the effects of probiotics on gut health in participants free from significant health conditions. Fifty-four participants were randomly assigned to receive either a placebo or composite probiotics for 60 d. Shotgun metagenomics revealed that individuals with lower baseline Gut Microbiome Wellness Index 2 (GMWI) exhibited more decisive responses to probiotic intervention, characterized by an increased abundance of beneficial commensal bacteria, including Adlercreutzia equolifaciens. Probiotic intake significantly improved the function of the gut microbiome, reducing antibiotic resistance genes and virulence factors while enhancing carbohydrate-active enzymes. Notably, A. equolifaciens promoted the production of palmitoyl serinol, a metabolite associated with improved GMWI and preventive benefits in blood glucose. In a population-based experiment, these findings were validated in a follow-up single-strain probiotic intervention with Lacticaseibacillus casei Zhang. Our study highlights the potential of probiotics as an early intervention strategy for maintaining gut health in individuals without significant health conditions.}, } @article {pmid40514168, year = {2025}, author = {Ebrahimi, F and Maleki, H and Ebrahimi, M and Beiki, AH}, title = {A novel approach to finding the compositional differences and biomarkers in gut microbiota in type 2 diabetic patients via meta-analysis, data-mining, and multivariate analysis.}, journal = {Endocrinologia, diabetes y nutricion}, volume = {72}, number = {6}, pages = {501561}, doi = {10.1016/j.endien.2025.501561}, pmid = {40514168}, issn = {2530-0180}, mesh = {Female ; Humans ; Male ; Middle Aged ; Biomarkers/analysis ; *Data Mining ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Multivariate Analysis ; }, abstract = {Type 2 diabetes mellitus (T2DM)-one of the fastest globally spreading diseases-is a chronic metabolic disorder characterized by elevated blood glucose levels. It has been suggested that the composition of gut microbiota plays key roles in the prevalence of T2DM. In this study, a novel approach of large-scale data mining and multivariate analysis of the gut microbiome of T2DM patients and healthy controls was conducted to find the key compositional differences in their microbiota and potential biomarkers of the disease.

METHODS: First, suitable datasets were identified (9 in total with 946 samples), analyzed, and their operational taxonomic units (OTUs) were computed by identical parameters to increase accuracy. The following OTUs were merged and compared based on their health status, and compositional differences detected. For biomarker identification, the OTUs were subjected to 9 different attribute weighting models. Additionally, OTUs were independently analyzed by multivariate algorithms (LEfSe test) to verify the realized biomarkers.

RESULTS: Overall, 23 genera and 4 phyla were identified as possible biomarkers. At genus level, the decrease of Bacteroides, Methanobrevibacter, Paraprevotella, and [Eubacterium] hallii group in T2DM and the increase of Prevotella, Megamonas, Megasphaera, Ligilactobacillus, and Lachnoclostridium were selected as biomarkers; and at phylum level, the increase of Synergistota and the decrease of Euryarchaeota, Desulfobacterota (Thermodesulfobacteriota), and Ptescibacteria.

CONCLUSION: This is the first study ever conducted to find the microbial compositional differences and biomarkers in T2DM using data mining models applied on a widespread metagenome dataset and verified by multivariate analysis.}, } @article {pmid40510676, year = {2025}, author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F}, title = {Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1515939}, pmid = {40510676}, issn = {1664-302X}, abstract = {Iron overload disorder (IOD) is a common condition in ex-situ black rhinoceroses (Diceros bicornis), although it has not been reported in the wild. This study aimed to gain a deeper understanding of the relationship between 25-hydroxy vitamin D [25(OH)D], inflammatory markers, insulin levels, the gut microbiome, dietary components, and transferrin saturation (TS) in ex-situ black rhinoceroses. Blood and fecal samples from 11 black rhinoceroses at five different European zoological institutions were monitored over a 1-year period. Inflammatory markers such as interleukin 6 (IL-6), serum amyloid A (SAA), interferon γ (IFN-γ), and tumor necrosis factor α (TNF-α) were analyzed. Our study corroborates the findings of previous research, which demonstrated that insulin, inflammatory markers, and TS% are higher in ex-situ black rhinoceroses compared to published wild ranges. Our data show no correlations between insulin, 25(OH)D, TS%, inflammatory markers, or short-chain fatty acids (SFCAs). Serum 25(OH)D exhibited significantly higher levels in summer than in winter. Transferrin saturation was influenced by age, which is consistent with previous studies. The microbiome did not differ significantly among individuals, institutions, sex, or season, unlike the mycobiome, which exhibited significant differences across institutions. The impact of the mycobiome differences on the physiology of the animals could not be determined from this study.}, } @article {pmid40508035, year = {2025}, author = {Toto, F and Scanu, M and Gramegna, M and Putignani, L and Del Chierico, F}, title = {Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples.}, journal = {International journal of molecular sciences}, volume = {26}, number = {11}, pages = {}, pmid = {40508035}, issn = {1422-0067}, support = {Current Research funds//Italian Ministry of Health/ ; n.a.//Technogenetics S.p.A./ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *DNA, Bacterial/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Bacteria/genetics/classification ; Metagenome ; }, abstract = {High-throughput 16S rRNA metagenomic sequencing has advanced our understanding of the gut microbiome, but its reliability depends on upstream processes such as DNA extraction and bacterial library preparation. In this study, we evaluated the impact of three different DNA extraction methods (a manual method with an ad hoc-designed pre-extraction phase (PE-QIA), and two automated magnetic bead-based methods (T180H and TAT132H)) and two bacterial library preparation protocols (home brew and VeriFi) on the 16S rRNA-based metagenomic profiling of faecal samples. T180H and TAT132H produced significantly higher DNA concentrations than PE-QIA, whereas TAT132H yielded DNA of lower purity compared to the others. In the taxonomic analysis, PE-QIA provided a balanced recovery of Gram-positive and Gram-negative bacteria, TAT132H was enriched in Gram-positive taxa, and T180H was enriched in Gram-negative taxa. An analysis of Microbial Community Standard (MOCK) samples showed that PE-QIA and T180H were more accurate than TAT132H. Finally, the VeriFi method yielded higher amplicon concentrations and sequence counts than the home brew protocol, despite the high level of chimeras. In conclusion, a robust performance in terms of DNA yield, purity, and taxonomic representation was obtained by PE-QIA and T180H. Furthermore, it was found that the impact of PCR-based steps on gut microbiota profiling can be minimized by an accurate bioinformatic pipeline.}, } @article {pmid40507096, year = {2025}, author = {Lutsiv, T and Fitzgerald, VK and Neil, ES and McGinley, JN and Hussan, H and Thompson, HJ}, title = {Cooked Bean (Phaseolus vulgaris L.) Consumption Alters Bile Acid Metabolism in a Mouse Model of Diet-Induced Metabolic Dysfunction: Proof-of-Concept Investigation.}, journal = {Nutrients}, volume = {17}, number = {11}, pages = {}, pmid = {40507096}, issn = {2072-6643}, support = {58-3060-8-031//USDA ARS/ ; 2020-05206//National Institute for Food and Agriculture:/ ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; *Phaseolus ; Mice ; Male ; Liver/metabolism ; Disease Models, Animal ; Feces/chemistry ; Cecum/microbiology/metabolism ; Gastrointestinal Microbiome ; Cooking ; Obesity/metabolism ; Metabolomics ; *Diet ; *Metabolic Diseases/etiology/metabolism ; Diet, High-Fat/adverse effects ; }, abstract = {Background/Objectives: Metabolic dysregulation underlies a myriad of chronic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD) and obesity, and bile acids emerge as an important mediator in their etiology. Weight control by improving diet quality is the standard of care in prevention and control of these metabolic diseases. Inclusion of pulses, such as common bean, is an affordable yet neglected approach to improving diet quality and metabolic outcomes. Thus, this study evaluated the possibility that common bean alters bile acid metabolism in a health-beneficial manner. Methods: Using biospecimens from several similarly designed studies, cecal content, feces, liver tissue, and plasma samples from C57BL/6 mice fed an obesogenic diet lacking (control) or containing cooked common bean were subjected to total bile acid analysis and untargeted metabolomics. RNA-seq, qPCR, and Western blot assays of liver tissue complemented the bile acid analyses. Microbial composition and predicted function in the cecal contents were evaluated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Results: Bean-fed mice had increased cecal bile acid content and excreted more bile acids per gram of feces. Consistent with these effects, increased synthesis of bile acids in the liver was observed. Microbial composition and capacity to metabolize bile acids were markedly altered by bean, with greater prominence of secondary bile acid metabolites in bean-fed mice, i.e., microbial metabolites of chenodeoxycholate/lithocholate increased while metabolites of hyocholate were reduced. Conclusions: In rendering mice resistant to obesogenic diet-induced MASLD and obesity, cooked bean consumption sequesters bile acids, increasing their hepatic synthesis and enhancing their diversity through microbial metabolism. Bean-induced changes in bile acid metabolism have potential to improve dyslipidemia.}, } @article {pmid40507017, year = {2025}, author = {Ying, J and Xu, X and Zhou, R and Chung, ACK and Ng, SK and Fan, X and Subramaniam, M and Wong, SH}, title = {The Gut Microbiota in Young Adults with High-Functioning Autism Spectrum Disorder and Its Performance as Diagnostic Biomarkers.}, journal = {Nutrients}, volume = {17}, number = {11}, pages = {}, pmid = {40507017}, issn = {2072-6643}, support = {Nil//NHG-LKCMedicine Clinician-Scientist Preparatory Programme Plus/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/microbiology/diagnosis ; Male ; Female ; Biomarkers ; Young Adult ; Adult ; Case-Control Studies ; Feces/microbiology ; Metagenomics ; Machine Learning ; ROC Curve ; Adolescent ; }, abstract = {Background/Objectives: Diagnosing ASD in adults presents unique challenges, and there are currently no specific biomarkers for this condition. Most existing studies on the gut microbiota in ASD are conducted in children; however, the composition of the gut microbiota in children differs significantly from that of adults. This study aimed to study the gut microbiota of young adults with high-functioning ASD. Methods: Using metagenomic sequencing, we evaluated the gut microbiota in 45 adults with high-functioning ASD and 45 matched healthy controls. Results: Adjusting for sociodemographic information, dietary habits, and clinical data, we observed a distinct microbiota profile of adults with ASD in comparison to controls, with the intensity of autistic traits strongly correlating to microbial diversity (correlation coefficient = -0.351, p-value < 0.001). Despite a similar dietary pattern, the ASD group exhibited more gastrointestinal symptoms than the healthy controls. An internally validated machine-learning predictive model that combines the Autism Spectrum Quotient questionnaire score of individuals with their microbial features could achieve an area under the receiver operating characteristic curve (AUC) of 0.955 in diagnosing ASD in adults. Conclusions: This study evaluates the gut microbiota in adult ASD and highlights its potential as a non-invasive biomarker to enhance the diagnosis of ASD in this population group.}, } @article {pmid40506497, year = {2025}, author = {Jung, DR and Choi, Y and Jeong, M and Singh, V and Jeon, SY and Seo, I and Park, NJ and Lee, YH and Park, JY and Han, HS and Shin, JH and Chong, GO}, title = {Metagenomic insight into the vaginal microbiome in women infected with HPV 16 and 18.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {105}, pmid = {40506497}, issn = {2055-5008}, mesh = {Female ; Humans ; *Vagina/microbiology/virology ; *Human papillomavirus 16/genetics/isolation & purification ; *Papillomavirus Infections/virology/microbiology ; *Microbiota/genetics ; Metagenomics ; *Human papillomavirus 18/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Uterine Cervical Neoplasms/virology/microbiology ; Metagenome ; Adult ; Middle Aged ; }, abstract = {Human papillomavirus (HPV) 16 and 18 (HPV 16/18) account for over 70% of cervical cancer (CC) cases, yet their interaction with the vaginal microbiome (VM) remains unclear. This study explored the association between high-risk HPV types (HR-HPVs), VM composition and bacterial function using shotgun metagenomic sequencing. In early-stage cervical lesions, the HPV 16/18 group showed reduced Lactobacillus-dominant community state types compared to other HR-HPVs, while invasive CC exhibited increased pathogenic bacteria, including Streptococcus agalactiae, Fannyhessea vaginae, and Sneathia vaginalis. The VM associated with HPV 16/18 was enriched in immune response and inflammation pathways, whereas other HR-HPVs were linked to cellular metabolism and hormonal signaling. Notably, HPV 16/18 exhibited stronger bacterial-fungal correlations, indicating shifts in the microbial community. Furthermore, 137 metagenome-assembled genomes provided insights into unique microbial genomic signatures. Our study links VM differences with HPV 16/18 oncogenic potential across cervical lesion stages, urging further research for better diagnostics and treatments.}, } @article {pmid40506443, year = {2025}, author = {Bredon, M and Hausfater, P and Khalki, L and Tijani, Y and Cheikh, A and Brot, L and Creusot, L and Rolhion, N and Trottein, F and Lambeau, G and Georgin-Lavialle, S and Bleibtreu, A and Baudel, JL and Lefèvre, A and Emond, P and Tubach, F and Simon-Tillaux, N and Simon, T and Gorochov, G and Zaid, Y and Sokol, H}, title = {Gut microbiota alterations are linked to COVID-19 severity in North African and European populations.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {106}, pmid = {40506443}, issn = {2055-5008}, support = {ANR-23-CE15-0014-01, GUTSY//AAP générique 2022/ ; ANR-23-CE15-0014-01, GUTSY//AAP générique 2022/ ; PR-BLV-20220527//Balvi Filantropic Fund/ ; RPH20003DDP//DIM One Health 2020/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; *COVID-19/microbiology/pathology ; *Dysbiosis/microbiology ; Feces/microbiology ; France/epidemiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Morocco/epidemiology ; North African People ; Severity of Illness Index ; }, abstract = {Although COVID-19 primarily affects the respiratory system, many patients experience gastrointestinal symptoms, suggesting a role for the gut microbiota in disease pathogenesis. To explore this, we performed shotgun metagenomic sequencing on stool samples from 200 COVID-19 patients and 102 healthy controls in Morocco and France. Despite geographic differences in microbiota composition, patients with COVID-19 in both continents exhibited significant gut microbiota alterations, which were more pronounced in severe cases, with similar features compared with controls. Functional pathways, including L-Tryptophan biosynthesis, were disrupted, particularly in patients with severe disease. Machine learning models accurately predicted disease severity based on gut microbial profiles in the Moroccan cohort, though not in the French cohort. These results highlight consistent microbiota changes associated with COVID-19 and support a potential link between gut dysbiosis and disease severity.}, } @article {pmid40503898, year = {2025}, author = {Han, H and Ji, M and Li, Y and Gong, X and Song, W and Zhou, J and Ma, K and Zhou, Y and Liu, X and Wang, M and Li, Y and Tu, Q}, title = {Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0041325}, pmid = {40503898}, issn = {2379-5077}, support = {32371598//National Natural Science Foundation of China/ ; 2020YFA0607600//National Key Research and Development Program of China/ ; }, mesh = {*Metagenome/genetics ; *Eukaryota/genetics/classification ; *Biodiversity ; RNA, Ribosomal, 18S/genetics ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; Phylogeny ; Seashore ; }, abstract = {Eukaryotes, both micro- and macro-, constitute the dominant component of Earth's biosphere visible to the naked eye. Although relatively big in organismal size, tracing eukaryotic diversity in complex environments is not easy. For example, they may actively escape from sampling and be physically absent from the collected samples. In this study, we strived to recover non-fungal eukaryotic DNA sequences from typical shotgun metagenomes in the complex mudflat intertidal zones. Multiple recently developed approaches for identifying eukaryotic sequences from shotgun metagenomes were comparatively assessed. Considering the low overlap among different approaches, an integrative workflow was proposed. The integrative workflow was then used to recover the eukaryotic communities in complex intertidal sediments. The temporal dynamics of intertidal eukaryotic communities were investigated through a time-series sampling effort. Thirty-four non-fungal eukaryotic phyla were detected from 36 shotgun metagenomes. Clear temporal variation in relative abundance was observed for eukaryotic genera such as Timema and Navicula. Strong temporal turnover of intertidal eukaryotic communities was observed. By comparing to 18S rRNA gene amplicon sequencing, dramatically different community profiles were observed between these two approaches. However, the temporal patterns for intertidal eukaryotic communities recovered by both approaches were generally comparable. This study provides valuable technical insights into the recovery of non-fungal eukaryotic information from complex environments and demonstrates an alternative route for reusing the massive metagenomic data sets generated in the past and future.IMPORTANCEEukaryotes represent the dominant component visible to the naked eye and contribute to the primary biomass in the Earth's biosphere. Yet, tracing the eukaryotic diversity in complex environments remains difficult, as they can actively move around and escape from sampling. Here, using the intertidal sediments as an example, we strived to retrieve non-fungal eukaryotic sequences from typical shotgun metagenomes. Compared to 18S rRNA gene amplicon sequencing, the shotgun metagenome-based approach resolved dramatically different eukaryotic community profiles, though comparable ecological patterns could be observed. This study paves an alternative way for utilizing shotgun metagenomic data to recover non-fungal eukaryotic information in complex environments, demonstrating significant potential for environmental monitoring and biodiversity investigations.}, } @article {pmid40500753, year = {2025}, author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A}, title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {163}, pmid = {40500753}, issn = {1474-760X}, support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; }, mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; }, abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.}, } @article {pmid40499078, year = {2025}, author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z}, title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.}, journal = {Journal of proteome research}, volume = {24}, number = {7}, pages = {3429-3446}, doi = {10.1021/acs.jproteome.5c00108}, pmid = {40499078}, issn = {1535-3907}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Polymorphism, Single Nucleotide ; *Amino Acids/genetics ; Metagenome/genetics ; Inflammatory Bowel Diseases/microbiology/genetics ; Diabetes Mellitus, Type 1/microbiology/genetics ; Proteome/genetics ; }, abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.}, } @article {pmid40497681, year = {2025}, author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J}, title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0057325}, pmid = {40497681}, issn = {2165-0497}, support = {OPP1019093//Bill and Melinda Gates Foundation/ ; }, mesh = {Humans ; *Feces/microbiology ; *Shigella/genetics/isolation & purification/pathogenicity/classification ; *Dysentery, Bacillary/microbiology/diagnosis ; Child, Preschool ; *Diarrhea/microbiology ; Infant ; Virulence Factors/genetics ; Female ; Male ; *Gastrointestinal Microbiome ; Child ; Developing Countries ; }, abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.}, } @article {pmid40497237, year = {2025}, author = {Feng, Y and Kuang, G and Pan, Y and Wang, J and Yang, W and Wu, WC and Pan, H and Wang, J and Han, X and Yang, L and Xin, GY and Shan, YT and Gou, QY and Liu, X and Guo, D and Liang, G and Holmes, EC and Gao, Z and Shi, M}, title = {Small mammals in a biodiversity hotspot harbor viruses of emergence risk.}, journal = {National science review}, volume = {12}, number = {6}, pages = {nwae463}, pmid = {40497237}, issn = {2053-714X}, abstract = {Metagenomic sequencing has transformed the understanding of viral diversity in wildlife and the potential threats these viruses pose to human health. Despite this progress, such sequencing studies often have lacked systematic and ecologically informed sampling, thereby likely missing many potential human pathogens and the drivers behind their ecology, evolution and emergence. We conducted an extensive search for viruses in the lungs, spleens and guts of 1688 mammals from 38 species across 428 sites in Yunnan Province, China-a hotspot for zoonoses emergence. We identified 162 mammalian viruses, including 102 new ones and 24 posing potential risks to humans due to their relationships with known human pathogens associated with serious diseases or their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-host associations, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.}, } @article {pmid40495477, year = {2025}, author = {Hurst, C and Zobel, G and Young, W and Olson, T and Parkar, N and Bracegirdle, J and Hannaford, R and Anderson, RC and Dalziel, JE}, title = {Social Isolation Induces Sex-Specific Differences in Behavior and Gut Microbiota Composition in Stress-Sensitive Rats.}, journal = {Brain and behavior}, volume = {15}, number = {6}, pages = {e70621}, pmid = {40495477}, issn = {2162-3279}, support = {//Smarter Lives: New opportunities for dairy products across the lifespan/ ; C10X1706//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Rats ; *Social Isolation/psychology ; *Stress, Psychological/microbiology/physiopathology ; *Behavior, Animal/physiology ; Rats, Inbred WKY ; Anxiety ; *Sex Characteristics ; Sex Factors ; Cecum/microbiology ; }, abstract = {BACKGROUND: Social isolation (SI) is an established rat model of chronic stress. We applied this to the stress-sensitive Wistar Kyoto (WKY) strain to explore brain-to-gut interactions associated with mood. Whether SI stress-induced behavioral changes are sex-specific or if they affect the microbiome in WKY is unknown. We hypothesized individually housed (IH) animals would be more anxious than pair-housed (PH), with sex differences. Male and female rats were either IH or PH from 70 to 112 days old and behavior was assessed in modified open field (OFTmod), elevated plus maze (EPM), and novel object recognition (NOR) tests. Cecal content DNA was analyzed by shotgun metagenome sequencing.

RESULTS: IH rats, particularly females, spent more time in the center of the OFTmod where the semi-novel feed was presented compared to PH group rats. There was a tendency for greater distance traveled, or potential hyperactivity, in IH female rats. Males stayed in the EPM closed arms more than females. No treatment difference occurred for recognition memory. SI altered cecal microbiome composition in females where housing was associated with seven differentially abundant taxa and 49 differentially abundant KEGG Level 3 ortholog/gene categories. Several relationships were noted between behavioral traits and relative abundance of microbiome taxa. There was a greater shift in female microbiome composition.

CONCLUSIONS: In summary, behavioral responses to the housing treatment were minimal. IH animals, particularly females, spent more time in the center of an OFT that contained food; this may have been an indication of depression, as opposed to anxiety. Housing status had a differential impact on the microbiome for females compared to males. The associations between cecal microbiota and activity in the modified OFT suggest that dietary interventions that influence the relative abundance of Bifidobacteria, Alistipes, and Muribaculaceae should be explored.}, } @article {pmid40494644, year = {2025}, author = {Ma, R and Shi, Y and Wu, W and Huang, C and Xue, F and Hou, R and Zhou, Y and Gu, J and Feng, F and Yu, X and Liu, J and Li, Z and Zhang, L and Lan, G and Chen, C and Bi, W and Song, X and Fu, M and Yang, H and Gu, H and Yang, J and Qi, D}, title = {The bacterial diversity and potential pathogenic risks of giant panda-infesting ticks.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0219724}, pmid = {40494644}, issn = {2165-0497}, support = {U21A20193//National Natural Science Foundation of China/ ; 32400405//National Natural Science Foundation of China/ ; 2023NSFSC1156//Sichuan Science and Technology Program/ ; 2024NSFSC0023//Sichuan Science and Technology Program/ ; 2023-YF09-00017-SN//Chengdu Science and Technology Bureau/ ; 2024CPB-A23, 2024CPB-Y05, CAZG2025C13//Chengdu Giant Panda Breeding Research Foundation/ ; }, mesh = {Animals ; *Ursidae/parasitology/microbiology ; Female ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; RNA, Ribosomal, 16S/genetics ; Male ; *Ticks/microbiology ; *Tick Infestations/veterinary/parasitology/microbiology ; Seasons ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Microbiota ; }, abstract = {UNLABELLED: As common parasites in the wild, ticks significantly limit the population growth of wild giant pandas and hinder the process of reintroducing captive giant pandas into their natural habitats. Research on microbial communities and pathogens in ticks infesting giant pandas is limited, emphasizing the need for a comprehensive investigation. To thoroughly investigate the microbial communities in giant panda-infesting ticks, particularly potential pathogens, we analyzed 246 ticks collected from the ears of wild-living giant pandas using 16S rRNA and metagenomic sequencing. We found that the microbial diversity in female ticks was significantly enriched in summer. The microbial community structure carried by ticks is more significantly influenced by seasonal changes than by sex. Metagenomic results indicated that giant pandas have a higher risk of Coxiella burnetii infection in summer and a higher risk of Anaplasma phagocytophilum, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Rickettsia amblyommatis infections in autumn. Over 90% of the ticks carried pathogens, with 82.54% harboring a single potentially pathogenic symbiont and the remaining 17.46% carrying multiple pathogens, all involving Coxiella burnetii. Using the CARD database, we identified a total of 121 antibiotic resistance genes (ARGs), with 76% exhibiting antibiotic efflux mechanisms. Based on the significantly associated ARGs, we provided antibiotic treatment recommendations for infections potentially caused by pathogenic symbionts. This study provides a clear answer to the potential microbial pathogen risks of ticks infesting giant pandas and offers a framework for tick-borne diseases in reintroduced wild panda populations.

IMPORTANCE: Importance: The emergence of tick-borne bacterial diseases poses a serious threat to the population health of wild-living giant pandas. Ticks are obligate hematophagous ectoparasites that survive by feeding on the blood of various animal hosts and spreading pathogens. Although some previous studies have confirmed that wild ticks carried various viruses, the role of wild giant panda-infesting ticks in the bacterial community remains unknown. Here, the identification of the microbial community and antibiotic resistome in giant panda-infesting ticks revealed that most Ixodes ovatus ticks are potentially pathogenic symbionts, including Anaplasma phagocytophilum, Coxiella burnetii, and Rickettsia amblyommatis. Tick-borne disease control also needs to take into account the effects of season, sex, and antibiotic efflux resistance genes. Our findings highlight the contribution of the scientific management of tick-borne diseases in the giant panda population.}, } @article {pmid40494297, year = {2025}, author = {Hibbett, D and Nagy, LG and Nilsson, RH}, title = {Fungal diversity, evolution, and classification.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {R463-R469}, doi = {10.1016/j.cub.2025.01.053}, pmid = {40494297}, issn = {1879-0445}, mesh = {*Fungi/classification/genetics ; Phylogeny ; *Biodiversity ; *Biological Evolution ; }, abstract = {Fungi include mushrooms, molds, lichens, yeasts, and zoosporic forms that occur as free-living or symbiotic organisms in every ecosystem on Earth. About 155,000 species of Fungi have been described, and possibly millions more remain to be named. Recent focus on aquatic habitats has illuminated major groups near the boundary between Fungi and protists. Fungal systematists have made remarkable progress toward resolving the major branches of the phylogeny, although some deep nodes have proven recalcitrant. Fungal taxonomists steadily describe about 3,000 new species per year, and fungal molecular ecologists routinely detect many thousands of unidentifiable 'dark fungi' through metagenomic analyses. To assemble the complete fungal tree of life, it will be necessary to connect the main branches of the phylogeny to information on all described species and integrate the vast and rapidly growing corpus of dark fungi.}, } @article {pmid40493399, year = {2025}, author = {Han, S and Zhang, Q and Zhang, H and Ma, J}, title = {Eucommia ulmoides and its inhibitory effects on prevotella in piglet gut microbiome through metagenomic and metabolomic analysis.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2503753}, doi = {10.1080/10495398.2025.2503753}, pmid = {40493399}, issn = {1532-2378}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Prevotella/drug effects ; Swine/microbiology/growth & development ; *Eucommiaceae/chemistry ; Animal Feed/analysis ; Metagenomics ; Metabolomics ; Diet/veterinary ; Dietary Supplements ; Feces/microbiology ; }, abstract = {Eucommia ulmoides (EU) is a traditional medicinal plant widely cultivated across China. The combination of EU and feed significantly affects the growth performance, intestinal microbiota composition, and metabolic characteristics of weaned piglets. Forty Landrace x Yorkshire piglets were randomly assigned to four groups: a control group receiving a basal diet, three treatment groups receiving a basal diet supplemented with EU and EU with mix energy (EU+ME), and EU with high protein and energy (EU+HPE), respectively. Growth performance was monitored over a 25-day feeding period, and fecal samples were collected for subsequent metagenomic sequencing and metabolomic analysis. Piglets supplemented with EU, EU+ME, and EU+HPE exhibited significantly improved growth performance, compared to the control group. Metagenomic analysis revealed significant alterations in gut microbiota composition, with increased beneficial bacterial classes and suppression of Prevotella spp. Metabolomic profiling demonstrated distinct metabolic alterations among the treatment groups, with pathway impact analysis highlighting enhanced protein synthesis and energy metabolism. Furthermore, EU supplementation did not affect porcine epidemic diarrhea virus activity in vitro but reduced LPS-induced intestinal inflammation. These findings suggest that EU could be a promising natural additive for improving piglet health and growth, with potential implications for managing post-weaning challenges in swine production.}, } @article {pmid40492742, year = {2025}, author = {Edwin, NR and Duff, A and Deveautour, C and Brennan, F and Abram, F and O'Sullivan, O}, title = {Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0105924}, pmid = {40492742}, issn = {2379-5077}, support = {2020019//Teagasc - the Agriculture and Food Development Authority/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine, Ireland/ ; 15S655//Department of Agriculture, Food and the Marine, Ireland/ ; }, mesh = {*Soil Microbiology ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; Ireland ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Grassland ; Soil/chemistry ; Phylogeny ; }, abstract = {Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.}, } @article {pmid40491436, year = {2025}, author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH}, title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1565887}, pmid = {40491436}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation & purification ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; }, abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.

METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.

RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6 months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).

CONCLUSION: These findings highlight the significant long-term impacts of mild COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.}, } @article {pmid40490984, year = {2025}, author = {Vargas, BO and Carazzolle, MF and Galhardo, JP and José, J and de Souza, BC and Correia, JBL and Santos, JRD and Pereira, GAG and de de Mello, FDSB}, title = {Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production.}, journal = {Biotechnology journal}, volume = {20}, number = {6}, pages = {e70050}, pmid = {40490984}, issn = {1860-7314}, support = {//National Agency of Petroleum, Natural Gas and Biofuels/ ; JPG: 88887.479699/2020-0//National Council for the Improvement of Higher Education/ ; JRS: 142340/2020-0//National Council for the Improvement of Higher Education/ ; BCS: 2022/05001-4//Fundação de Amparo à Pesquisa no Estado de São Paulo/ ; }, mesh = {*Saccharomyces cerevisiae/genetics/metabolism/enzymology ; Animals ; *Rumen/microbiology ; *Biofuels ; Sheep ; Xylose/metabolism ; Cattle ; Camelus/microbiology ; *Metabolic Engineering/methods ; Ethanol/metabolism ; Fermentation ; Microbiota/genetics ; Aldose-Ketose Isomerases ; }, abstract = {Xylose metabolism in Saccharomyces cerevisiae remains a significant bottleneck due to the difficulty in identifying functional and efficient xylose isomerases (XI). In the present study, publicly available metagenomic and metatranscriptomic datasets of rumen microbiota from different herbivorous mammals were used to prospect novel XIs sequences. Seven putative XIs from moose, camel, cow, and sheep were cloned into a strain modified for xylose metabolism. Out of those, five XIs demonstrated activity and efficiently converted xylose into xylulose, resulting in ethanol as the final product. A XI from camel rumen microbiota exhibited a KM of 16.25 mM, indicating high substrate affinity. The strains expressing enzymes XI11 and XI12, obtained from sheep rumen microbiota, were able to deplete 40 g/L of xylose within 72 and 96 h, achieving theoretical ethanol yields of 90% and 88%, respectively. These results are comparable to those obtained with Orpinomyces sp. ukk1 XI, a benchmark enzyme previously reported as highly efficient in S. cerevisiae. This study also provides the first report on the successful expression of XIs mined from the ruminal microbiotas of sheep and camels in S. cerevisiae, expanding the perspectives for the optimization of fermentation processes and the production of lignocellulosic biofuels from xylose.}, } @article {pmid40490486, year = {2025}, author = {Hendricks, H and Israel, S and Weitkamp, JH and Pakala, S and Rajagopala, S and Banerjee, R}, title = {Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia.}, journal = {Journal of perinatology : official journal of the California Perinatal Association}, volume = {45}, number = {7}, pages = {986-992}, pmid = {40490486}, issn = {1476-5543}, support = {UL1 TR002243/TR/NCATS NIH HHS/United States ; 5UL1TR002243-03//Vanderbilt Institute for Clinical and Translational Research (VICTR)/ ; }, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; *Bacteremia/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Infant, Premature ; Female ; Male ; Prospective Studies ; *Dysbiosis/microbiology ; Case-Control Studies ; Feces/microbiology ; Enterococcus/isolation & purification ; *Infant, Premature, Diseases/drug therapy/microbiology ; }, abstract = {BACKGROUND: Neonatal microbiome dysbiosis is associated with infectious complications.

METHODS: Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months. Neonates with bacteremia (cases) were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI).

RESULTS: We analyzed 398 stools from 40 cases and 39 controls. Cases had lower α diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower α diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance.

CONCLUSIONS: Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower α diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications.}, } @article {pmid40489603, year = {2025}, author = {Cao, J and He, Q and Zhang, M and Zhou, R and Feng, C}, title = {Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.}, journal = {Polish journal of microbiology}, volume = {74}, number = {2}, pages = {131-142}, pmid = {40489603}, issn = {2544-4646}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Invasive Pulmonary Aspergillosis/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Aged ; Adult ; Metagenomics ; Case-Control Studies ; High-Throughput Nucleotide Sequencing ; Clinical Relevance ; }, abstract = {Gut microbiota acts on the lungs through the gut-lung axis and play an important role in lung diseases. However, there are no reports on the gut microbiota characteristics in patients with invasive pulmonary aspergillosis (IPA). We aimed to analyze changes in gut microbiota in IPA patients, correlate these changes with clinical indicators and disease prognosis, and explore the application value of these characteristic changes in diagnosing IPA. The objective was to provide a theoretical basis for preventing and treating individual immunity. We conducted metagenomic next-generation sequencing of fecal samples from 43 patients with IPA and 31 healthy controls to analyze changes in the gut microbiota of these patients. We also built a random forest model for diagnosing IPA based on the gut microbiota. Compared to healthy controls, IPA patients showed a decrease in gut microbiota diversity and metabolic levels. Changes in the microbiota were characterized by a significant reduction in anti-inflammatory species that produce short-chain fatty acids, such as Faecalibacterium, Blautia, Roseburia, Phocaeicola, and Bacteroides. In contrast, opportunistic pathogens, such as Enterococcus, Corynebacterium, Escherichia, Staphylococcus, Haemophilus, and Finegoldia, were significantly enriched. The classification model based on Clostridium fessum, Blautia wexlerae, Streptococcus pseudopneumoniae, Corynebacterium striatum, and Faecalibacterium prausnitzii showed high value in distinguishing patients with IPA from healthy controls. Patients with IPA exhibit gut microbiota imbalance. The gut microbiota can serve as a biomarker that helps in diagnosing IPA. Our findings support the potential use of gut microbiota as a target for IPA prevention and treatment.}, } @article {pmid40489326, year = {2025}, author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Zhang, W and Fang, H and Chen, J}, title = {Changes of respiratory microbiota associated with prognosis in pulmonary infection patients with invasive mechanical ventilation-supported respiratory failure.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2514093}, pmid = {40489326}, issn = {1365-2060}, mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Respiration, Artificial/methods/adverse effects ; Prognosis ; *Respiratory Insufficiency/therapy/microbiology/mortality ; Middle Aged ; Aged ; *Microbiota/genetics ; Intensive Care Units/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/microbiology/mortality ; Anti-Bacterial Agents/therapeutic use ; Risk Factors ; }, abstract = {BACKGROUND: Respiratory failure (RF) is an important cause of intensive care unit (ICU) admission and mortality due to respiratory diseases. This study aimed to evaluate the clinical performance of metagenomic next-generation sequencing (mNGS) testing in pathogen diagnosis, medication guidance and to explore dynamic changes in the respiratory microbiota associated with prognosis.

METHODS: This multicenter retrospective study enrolled ICU patients from five hospitals who underwent invasive mechanical ventilation (IMV) and had pathogenic microorganisms identified by both mNGS and conventional microbiological tests (CMT) from December 2021 to April 2024. Patients were classified into two groups based on discharge outcomes: survivors (n=122) and non-survivors (n=35).

RESULTS: Compared with the survivors, non-survivors had a significantly higher proportion of smokers, dyspnea, type I RF, blood urea nitrogen, and C-reactive protein (p < 0.05). All the above indicators were identified as independent risk factors for mortality, except for type I RF. mNGS showed a better performance for pathogen identification than CMT in both groups, and nearly 60% showed consistent results between the two methods. Among survivors, antibiotic adjustment was mainly based on mNGS results (35.25%), whereas non-survivors more frequently received adjustments based on mNGS and CMT results (34.29%). The richness and abundance of lung microorganisms in the non-survivors were significantly lower than those in the survivors (p < 0.05).

CONCLUSIONS: mNGS is a promising method for identifying pathogens in pulmonary infections in IMV-supported RF patients and for exploring changes in lung microbial composition to provide a reference for patient prognosis.}, } @article {pmid40489211, year = {2025}, author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C}, title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.}, journal = {ACS chemical neuroscience}, volume = {16}, number = {14}, pages = {2691-2706}, doi = {10.1021/acschemneuro.5c00254}, pmid = {40489211}, issn = {1948-7193}, mesh = {*Amyotrophic Lateral Sclerosis/metabolism/microbiology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/metabolism/microbiology ; Male ; *Metabolomics/methods ; Female ; Middle Aged ; Biomarkers/metabolism ; Aged ; Metagenomics/methods ; Feces/microbiology ; }, abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.}, } @article {pmid40488951, year = {2025}, author = {Liu, Y and Huang, G and Wei, F and Hu, Y}, title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.}, journal = {Science China. Life sciences}, volume = {68}, number = {8}, pages = {2408-2419}, doi = {10.1007/s11427-024-2933-1}, pmid = {40488951}, issn = {1869-1889}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Mammals/microbiology ; Bacteria/genetics/classification ; *Gastrointestinal Tract/microbiology/anatomy & histology ; Metagenomics/methods ; Metagenome ; }, abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.}, } @article {pmid40488467, year = {2025}, author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L}, title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0145924}, pmid = {40488467}, issn = {2165-0497}, support = {2024YFC3506300, 2024YFC3506303//National Key R&D Program of China/ ; }, mesh = {Humans ; *Prediabetic State/microbiology/metabolism ; *Metabolomics/methods ; *Gastrointestinal Microbiome/genetics ; Male ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Blood Glucose ; Multiomics ; }, abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.}, } @article {pmid40488405, year = {2025}, author = {Ricci, F and Leung, PM and Hutchinson, T and Nguyen-Dinh, T and Frank, AH and Hood, AVS and Salazar, VW and Eate, V and Wong, WW and Cook, PLM and Greening, C and McClelland, H}, title = {Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40488405}, issn = {1751-7370}, mesh = {*Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Carbon Cycle ; *Lakes/microbiology ; Photosynthesis ; Oxidation-Reduction ; Hydrogen/metabolism ; *Microbiota ; Phototrophic Processes ; *Nutrients/metabolism ; }, abstract = {Photosynthetic microbial mats are macroscopic microbial ecosystems consisting of a wide array of functional groups and microenvironments arranged along variable redox gradients. Light energy ultimately drives primary production and a cascade of daisy-chained metabolisms. Heterotrophic members of these communities remineralise organic material, decreasing net primary production, and returning nutrients to the aqueous phase. However, reduced inorganic and one-carbon substrates such as trace gases and those released as metabolic byproducts in deeper anoxic regions of the mat, could theoretically also fuel carbon fixation, mitigating carbon loss from heterotrophy and enhancing net primary production. Here, we investigated the intricate metabolic synergies that sustain community nutrient webs in a biomineralising microbial mat from a hypersaline lake. We recovered 331 genomes spanning 40 bacterial and archaeal phyla that influence the biogeochemistry of these ecosystems. Phototrophy is a major metabolism found in 17% of the genomes, but over 50% encode enzymes to harness energy from inorganic substrates and 12% co-encode chemosynthetic carbon fixation pathways that use sulfide and hydrogen as electron donors. We experimentally demonstrated that the microbial community oxidises ferrous iron, ammonia, sulfide, and reduced trace gas substrates aerobically and anaerobically. Furthermore, carbon isotope assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and organic matter production alongside photosynthesis. Chemosynthesis in microbial mats results from a complex suite of spatially organised metabolic interactions and continuous nutrient cycling, which decouples carbon fixation from the diurnal cycle, and enhances the net primary production of these highly efficient ecosystems.}, } @article {pmid40488306, year = {2025}, author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M}, title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2514137}, pmid = {40488306}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.}, } @article {pmid40484531, year = {2025}, author = {Hu, Q and Cheng, S and Qian, D and Wang, Y and Xie, G and Peng, Q}, title = {Identification of core microbial communities and their influence on flavor-oriented traditional fermented sour cucumbers.}, journal = {Food microbiology}, volume = {131}, number = {}, pages = {104810}, doi = {10.1016/j.fm.2025.104810}, pmid = {40484531}, issn = {1095-9998}, mesh = {Volatile Organic Compounds/metabolism/analysis ; Fermentation ; *Cucumis sativus/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Taste ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Flavoring Agents/metabolism ; Humans ; *Microbial Consortia ; Food Microbiology ; *Microbiota ; }, abstract = {Sour cucumber is a traditional fermented vegetable with global popularity, yet its fermentation process often leads to inconsistencies in quality and flavor due to the reliance on natural fermentation. This study identifies 12 core volatile organic compounds (VOCs) contributing to its unique flavor and investigates the key microbial species involved in the fermentation process. Using a synthetic microbial consortium constructed from core microbial species, we successfully replicated the flavor profile of naturally fermented sour cucumbers while enhancing safety by reducing nitrite levels. This approach also reduced bitterness and astringency, while improving sourness and umami, providing a robust framework for standardized production of high-quality fermented vegetables. These findings offer practical solutions for improving flavor quality and ensuring the safety of fermented foods.}, } @article {pmid40483623, year = {2025}, author = {Chi, Y and Luo, M and Ding, C}, title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {7}, pages = {89}, pmid = {40483623}, issn = {1572-9699}, support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; }, mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; }, abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.}, } @article {pmid40483486, year = {2025}, author = {Bergholm, J and Tessema, TS and Blomström, AL and Berg, M}, title = {Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {188}, pmid = {40483486}, issn = {1743-422X}, support = {2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; }, mesh = {Animals ; Cattle ; Ethiopia/epidemiology ; *Diarrhea/veterinary/virology ; *Virome ; Metagenomics ; *Cattle Diseases/virology ; Feces/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.

METHODS: Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.

RESULTS: The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.

CONCLUSIONS: To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.}, } @article {pmid40483244, year = {2025}, author = {Duong, JT and Hayden, HS and Verster, AJ and Pope, CE and Miller, C and Kelsi Penewit, and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Kelly, A and Schwarzenberg, SJ and Freedman, SD and Hoffman, LR}, title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {24}, number = {4}, pages = {792-800}, doi = {10.1016/j.jcf.2025.05.006}, pmid = {40483244}, issn = {1873-5010}, support = {K24 HL141669/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Cystic Fibrosis/drug therapy/microbiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Quinolones/administration & dosage/therapeutic use ; *Benzodioxoles/administration & dosage/therapeutic use ; Drug Combinations ; *Aminophenols/administration & dosage/therapeutic use ; *Indoles/administration & dosage/therapeutic use ; *Pyridines/administration & dosage/therapeutic use ; Adult ; *Gastrointestinal Microbiome/drug effects ; Leukocyte L1 Antigen Complex/analysis ; Chloride Channel Agonists/administration & dosage ; Adolescent ; *Pyrazoles/administration & dosage/therapeutic use ; *Dysbiosis/microbiology ; Young Adult ; Pyrrolidines/administration & dosage ; }, abstract = {BACKGROUND: People with cystic fibrosis (PwCF) often have fecal dysbioses relative to those without CF, characterized by increased pro-inflammatory microbiota and gastrointestinal (GI) inflammation as measured by fecal calprotectin, suggesting that inflammation contributes to CF GI disease. The multicenter observational PROMISE study (NCT04038047) found that calprotectin decreased in PwCF treated with elexacaftor/tezacaftor/ivacaftor (ETI). To better understand the dynamics between fecal dysbiosis and GI inflammation, we characterized the microbiomes of fecal samples from PROMISE and the relationships with calprotectin before, 1-month post, and 6-months post ETI.

METHODS: Fecal microbiota from participants ≥12 y/o were determined by shotgun metagenomic sequencing with random forest modeling and multivariate linear regression analysis to define relationships between microbiota, calprotectin, and deltaF508 genotype before and after ETI.

RESULTS: We analyzed 345 samples from 124 participants. At baseline, we observed community-level differences in the fecal microbiota among participants with abnormal compared to normal calprotectin. With ETI, the relative abundances of 7 bacterial species - Escherichia coli, Staphylococcus aureus, Clostridium scindens, Enterocloster clostridioformis, Clostridium butyricum, Anaeroglobus geminatus, and Ruminococcus gnavus - decreased significantly, correlating with calprotectin decrease. We detected community-level differences in the fecal microbiota based on CFTR genotype and a distinct pattern of microbiota change in F508del homozygous compared to heterozygous participants after ETI.

CONCLUSIONS: We identified 7 species for which fecal abundances decreased with ETI and correlated with calprotectin decrease, supporting a close relationship between fecal microbiota and inflammation in PwCF. Future work will define these relationships with metabolites and GI symptoms during long-term ETI therapy.}, } @article {pmid40482930, year = {2025}, author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H}, title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107791}, doi = {10.1016/j.micpath.2025.107791}, pmid = {40482930}, issn = {1096-1208}, mesh = {Biofilms/growth & development/drug effects ; Humans ; *Probiotics/pharmacology ; *Microbiota ; Enterococcus faecalis/drug effects ; *Homeostasis ; *Bacteria/isolation & purification/classification/genetics ; Streptococcus mutans/drug effects ; *Dental Pulp Cavity/microbiology ; Metagenomics ; Microscopy, Electron, Scanning ; }, abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.

METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.

RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.

CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.}, } @article {pmid40482668, year = {2025}, author = {Garcia-Mauriño, C and Shao, Y and Miltz, A and Lawley, TD and Rodger, A and Field, N}, title = {Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.}, journal = {The Lancet. Microbe}, volume = {6}, number = {8}, pages = {101072}, doi = {10.1016/j.lanmic.2024.101072}, pmid = {40482668}, issn = {2666-5247}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; Female ; *Respiratory Tract Infections/virology/microbiology/epidemiology ; Male ; Infant ; Prospective Studies ; Metagenomics ; Feces/microbiology ; Birth Cohort ; Hospitalization/statistics & numerical data ; United Kingdom/epidemiology ; }, abstract = {BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs).

METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs.

FINDINGS: 3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4-2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] >35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85-0·99]; Shannon Index adjusted HR 0·57 [0·33-0·98]; and Simpson Index adjusted HR 0·36 [0·11-1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B longum dominated; cluster 1 [mixed] 3·05 [1·25-7·41] and cluster 2 [B breve dominated] 2·80 [1·06-7·44]).

INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies.

FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.}, } @article {pmid40481853, year = {2025}, author = {Chaverri, P and Escudero-Leyva, E and Mora-Rojas, D and Calvo-Obando, A and González, M and Escalante-Campos, E and Mesén-Porras, E and Wicki-Emmenegger, D and Rojas-Gätjens, D and Avey-Arroyo, J and Campos-Hernández, M and Castellón, E and Moreira-Soto, A and Drexler, JF and Chavarría, M}, title = {Differential Microbial Composition and Fiber Degradation in Two Sloth Species (Bradypus variegatus and Choloepus hoffmanni).}, journal = {Current microbiology}, volume = {82}, number = {7}, pages = {327}, pmid = {40481853}, issn = {1432-0991}, support = {VI 809-C3-102//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; 57592642//Deutscher Akademischer Austauschdienst/ ; }, mesh = {Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Cellulose/metabolism ; *Dietary Fiber/metabolism ; *Fungi/classification/metabolism/genetics/isolation & purification ; Metagenomics ; }, abstract = {Sloths have the slowest digestion among mammals, requiring 5-20 times longer to digest food than other herbivores, which suggests differences in their gut microbiota, particularly in plant-fiber-degrading microorganisms. Bradypus variegatus has a lower metabolic rate and moves less than Choloepus hoffmanni. However, no comprehensive studies have compared the microbiota (e.g., fungi) of these species. We hypothesized that differences in digestion and metabolism between the two species would be reflected in their microbiota composition and functionality, which we characterized using metagenomics, metabarcoding, and cellulose degradation. Results revealed significant differences in microbiota composition and functionality. Both species are dominated by bacteria; fungi comprised only 0.06-0.5% of metagenomic reads. Neocallimastigomycota, an anaerobic fungus involved in fiber breakdown in other herbivores, was found in low abundance, especially in B. variegatus. Bacterial communities showed subtle differences: C. hoffmanni was dominated by Bacillota and Bacteroidota, while B. variegatus showed higher Actinomycetota. Expected herbivore bacterial taxa (e.g., Fibrobacter and Prevotella) were scarce. Functional analysis showed a low abundance of carbohydrate-active enzymes essential for polysaccharide breakdown. Cellulose degradation assays confirmed that sloths digest only ~ 3-30% of ingested plant material. This research sheds light on the potential multidirectional links between the gut microbiota, metabolism, and digestion.}, } @article {pmid40480048, year = {2025}, author = {Yang, J and Liu, J and Gu, H and Song, W and Zhang, H and Wang, J and Yang, P}, title = {Gut microbiota, metabolites, and pulmonary hypertension: Mutual regulation and potential therapies.}, journal = {Microbiological research}, volume = {299}, number = {}, pages = {128245}, doi = {10.1016/j.micres.2025.128245}, pmid = {40480048}, issn = {1618-0623}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Hypertension, Pulmonary/microbiology/therapy/metabolism ; Fatty Acids, Volatile/metabolism ; Methylamines/metabolism ; Animals ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics ; Tryptophan/metabolism ; }, abstract = {Pulmonary hypertension is a progressive condition characterized by increased pulmonary vascular pressure and resistance, ultimately leading to right heart failure and death. Increasing evidence has underscored the importance of the gut-lung axis in the development of respiratory and cardiovascular diseases. Notably, significant changes in the gut microbiota, including altered microbial composition and function, have been observed in pulmonary hypertension. Specifically, microbiota-derived metabolites, including short chain fatty acids, trimethylamine N-oxide, bile acids and tryptophan, play a significant role in the development of pulmonary hypertension. The identification of key bacteria and metabolites, along with recent advances in gut microbiota-targeting technologies and metabolic pathway-targeting inhibitors/agonists, holds potential for developing diagnostic, prognostic, and therapeutic strategies for pulmonary hypertension. Emerging research directions include metagenomic analysis of viruses and fungi, artificial intelligence-aided prediction models, novel metabolites and their associated enzymes, drug-microbiota interactions, selective antibiotics, and advanced microbiota transplantation. This review synthesizes clinical and experimental evidence linking the gut microbiota to pulmonary hypertension, highlighting their interplay as a promising avenue for further investigation and translational applications.}, } @article {pmid40478429, year = {2025}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Hydrological regime and niche partitioning drive fungal community structure and function in arid wetlands sediments of South Africa.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {25}, pages = {15217-15231}, pmid = {40478429}, issn = {1614-7499}, support = {DST/CON0197/2017//Department of Science and Innovation, South Africa/ ; }, mesh = {*Wetlands ; South Africa ; *Fungi ; *Geologic Sediments/microbiology ; Hydrology ; Mycobiome ; Mycorrhizae ; Ecosystem ; Biodiversity ; }, abstract = {Arid wetlands are ecologically significant yet understudied ecosystems shaped by extreme conditions and hydrological variability. However, the structure and ecological functional of fungal communities in these habitats remain poorly understood, especially in southern Africa. This study integrated shotgun metagenomics, FUNGuild functional profiling, and multivariate analyses to examine fungal diversity, functional composition, and environmental drivers in seasonal and permanent arid wetlands of South Africa. Distinct fungal assemblages emerged, primarily shaped by hydrological regimes and ionic stress. Seasonal wetlands were dominated by Mucoromycota (79%), particularly arbuscular mycorrhizal (AM) fungus (Rhizophagus, 62%), while permanent wetlands had higher Ascomycota (54%), with Aspergillus (50%) prevalent in oxygen-limited sediments. Although alpha diversity showed no significant difference, beta diversity confirmed significant mycobiome differentiation. Total dissolved solids (TDS), electrical conductivity (EC), and salinity were key predictors of fungal composition, with TDS the strongest determinant (p < 0.01). Functional guild analysis highlighted niche differentiation, with saprotrophs dominating permanent wetlands (59.7% vs. 21.5%; p < 0.05), while symbiotrophs, particularly AM fungi, were enriched in seasonal wetlands (69.3% vs. 36.1%; p < 0.001). Indicator taxa identified via LefSe (LDA > 3, p < 0.05) and random forest modeling included Rhizophagus, Trichoderma, Fusarium, and Entomophthora in seasonal wetlands, and Aspergillus in permanent wetlands. This study provides the first integrative insight into fungal ecology in South Africa's arid wetlands, demonstrating that hydrological regime shapes fungal structure and function through environmental filtering and niche specialization, with implications for guiding conservation and adaptive management of these fragile ecosystems.}, } @article {pmid40476734, year = {2025}, author = {Marcos-Zambrano, LJ and Lacruz-Pleguezuelos, B and Aguilar-Aguilar, E and Marcos-Pasero, H and Valdés, A and Loria-Kohen, V and Cifuentes, A and Ramirez de Molina, A and Diaz-Ruiz, A and Pancaldi, V and Carrillo de Santa Pau, E}, title = {Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.}, journal = {mSystems}, volume = {10}, number = {7}, pages = {e0014325}, pmid = {40476734}, issn = {2379-5077}, support = {TEC-2024/BIO-167 CD3DTech-CM (ORDER 5696/2024, B.O.C.M. No. 307 12/26/2024)//Comunidad de Madrid/ ; }, mesh = {Humans ; *Celiac Disease/microbiology/diet therapy/metabolism ; *Diet, Gluten-Free ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Cross-Sectional Studies ; Pilot Projects ; Severity of Illness Index ; Feces/microbiology ; Metabolome ; }, abstract = {UNLABELLED: Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient's microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled "Low-grade symptoms," displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named "High-grade symptoms," exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.

IMPORTANCE: Celiac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6-12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.}, } @article {pmid40475999, year = {2025}, author = {Hwang, D and Chong, E and Li, Y and Li, Y and Roh, K}, title = {Deciphering the gut microbiome's metabolic code: pathways to bone health and novel therapeutic avenues.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1553655}, pmid = {40475999}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Probiotics/therapeutic use ; *Bone Remodeling/physiology ; *Osteoporosis/metabolism/microbiology/therapy ; Prebiotics ; Fecal Microbiota Transplantation ; Bone Diseases/metabolism/microbiology/therapy ; }, abstract = {The gut microbiome plays an important role in the protection against various systemic diseases. Its metabolic products profoundly influence a wide range of pathophysiological events, including the regulation of bone health. This review discusses the recently established connections between the gut microbiome and bone metabolism, focusing on the impact of microbiome-derived metabolites such as SCFAs, Bile Acids, and tryptophan to the control of bone remodeling and immunoreactions. Recent advances in metagenomics and microbiome profiling have unveiled new exciting therapeutic opportunities, ranging from the use of probiotics, prebiotics, engineered microbes, and to fecal microbiota transplantation. Understanding of the interplay among diet, microbiota, and bone health provides new avenues for tailored interventions aimed at reducing disease risk in osteoporosis and other related disorders. By drawing knowledge from microbiology, metabolism, and bone biology, this review highlights the potential of microbiome-targeted therapies to transform skeletal health and the management of bone diseases.}, } @article {pmid40475346, year = {2025}, author = {Wang, Z and Wei, X and Piao, L and Zhang, X and Wang, H}, title = {Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1600470}, pmid = {40475346}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; China/epidemiology ; *Caliciviridae Infections/microbiology/virology ; *Norovirus ; Metagenomics ; Feces/microbiology ; Male ; Female ; *Gastroenteritis/virology/microbiology ; Child, Preschool ; Child ; Infant ; Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Norovirus (NoV) is a leading cause of acute gastroenteritis in pediatric populations worldwide. However, the role of gut microbiota in NoV pathogenesis remains poorly understood.

METHODS: We conducted a longitudinal metagenomic analysis of fecal samples from 12 NoV-infected children and 13 age-matched healthy controls in Northeast China. Microbial composition and functional pathways were assessed using high-throughput shotgun sequencing and bioinformatic profiling.

RESULTS: NoV infection was associated with significant gut microbial dysbiosis, including increased alpha diversity and distinct taxonomic shifts. Notably, Bacteroides uniformis, Veillonella spp., and Carjivirus communis were enriched in infected individuals. Functional analysis revealed upregulation of metabolic pathways involved in carbohydrate and lipid processing. These microbial and functional alterations persisted over time and correlated with disease severity.

CONCLUSIONS: Our findings reveal novel associations between NoV infection and gut microbiota dysbiosis, particularly the enrichment of Bacteroides uniformis, which may influence host-pathogen interactions via metabolic or immune mechanisms. The identified microbial and metabolic signatures offer potential biomarkers for diagnosis and targets for microbiota-based therapeutic strategies in pediatric NoV infection.}, } @article {pmid40473843, year = {2025}, author = {Wu, S and Wang, S and Wu, Z and Chen, M and Chen, X and Lei, D and Peng, C}, title = {Comparative analysis of the clinical characteristic and lung microbiota in adult and elderly patients with pulmonary tuberculosis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19777}, pmid = {40473843}, issn = {2045-2322}, support = {2023K146//Quzhou City science and technology plan project/ ; }, mesh = {Humans ; Middle Aged ; Male ; Female ; *Tuberculosis, Pulmonary/microbiology/diagnosis/diagnostic imaging ; Aged ; Adult ; *Lung/microbiology/diagnostic imaging ; *Microbiota/genetics ; Retrospective Studies ; Age Factors ; High-Throughput Nucleotide Sequencing ; Young Adult ; Aged, 80 and over ; }, abstract = {The proportion of elderly people infected with tuberculosis (TB) is increasing, and misdiagnosis and missed diagnosis are common. This study aimed to explore the diagnostic value of metagenomic next-generation sequencing (mNGS) for pulmonary TB (PTB) and to investigate age-related differences in lung microbial composition, clinical characteristics and imaging findings among PTB patients. We retrospectively recruited 162 suspected PTB patients, and finally 143 patients were used in this analysis. Patients were classified into two groups: adult (18 ≤ age < 60, n = 66) and elderly (Age ≥ 60, n = 77). Differences and associations in clinical characteristics, imaging findings, and lung microbiota were analyzed. Compared to adult patients, elderly patients had a higher prevalence of hypertension (31.17% vs. 9.09%, P = 0.0012), fever (20.78% vs. 4.55%, P = 0.0044) and chest tightness (24.68% vs. 10.61%, P = 0.0297), but a lower prevalence of chest pain (7.58% vs. 0%, P = 0.0139). For TB identification, mNGS had the highest positive rate (100%), followed by T-spot (74.75%), GeneXpert (37.80%) and acid-fast staining (AFS) (7.30%), and all the conventional methods showed slight higher positive rates in the elderly group compared to the adult group (P > 0.05). Bilateral lung infection was more common in elderly patients (79.22% vs. 60.61%, P = 0.0148), with infiltration (32.17%, 46/143), shadows (26.57%, 38/143), nodules (20.28%, 29/143), and bronchiectasis (20.28%, 29/143) being the most common imaging features. The diversity of the lung microbial communities was significantly lower in elderly patients compared to adults (P < 0.05). Clinical characteristics, imaging findings, and the top 20 most abundant species in lung microbiota showed significantly positive correlation. This study demonstrates that mNGS has excellent diagnostic value for PTB in both adult and elderly patients. Significant differences in clinical characteristics, imaging, and lung microbial composition were observed between the two groups. Understanding these differences may aid in the diagnosis and treatment of tuberculosis in elderly patients.}, } @article {pmid40473141, year = {2025}, author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X}, title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.}, journal = {Bioresource technology}, volume = {433}, number = {}, pages = {132770}, doi = {10.1016/j.biortech.2025.132770}, pmid = {40473141}, issn = {1873-2976}, mesh = {*Fermentation ; *Gene Transfer, Horizontal/genetics ; *Microbiota/genetics ; *Temperature ; Volatile Organic Compounds ; Bacteria/genetics/metabolism ; Phylogeny ; *Wine/microbiology ; *Adaptation, Physiological ; }, abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.}, } @article {pmid40473125, year = {2025}, author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF}, title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate hidradenitis suppurativa.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107778}, doi = {10.1016/j.micpath.2025.107778}, pmid = {40473125}, issn = {1096-1208}, mesh = {Humans ; *Hidradenitis Suppurativa/microbiology/pathology ; *Skin/microbiology/pathology ; *Fungi/isolation & purification/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Male ; Adult ; DNA, Fungal/genetics ; Prevalence ; Female ; Metagenomics ; Mycobiome ; Malassezia/isolation & purification/genetics ; Sequence Analysis, DNA ; Middle Aged ; }, abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.}, } @article {pmid40472755, year = {2025}, author = {Chen, M and Xing, L and Gao, S and Guo, Y and Qiu, T and Wang, X and Gao, M}, title = {Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities.}, journal = {Environment international}, volume = {201}, number = {}, pages = {109569}, doi = {10.1016/j.envint.2025.109569}, pmid = {40472755}, issn = {1873-6750}, mesh = {*Composting ; *Virulence Factors/genetics ; *Air Microbiology ; Metagenomics ; *Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Microbiota ; *Drug Resistance, Microbial/genetics ; Humans ; }, abstract = {The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.}, } @article {pmid40472396, year = {2025}, author = {Zheng, F and Guo, X and Zhang, W and Wang, Y and Hu, E and Guo, X and Su, H and Deng, C}, title = {Insights into the functional characteristics of rhubarb (Rheum officinale Baill) treatment on experimental traumatic brain injury through network pharmacology with metagenomics.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {143}, number = {}, pages = {156853}, doi = {10.1016/j.phymed.2025.156853}, pmid = {40472396}, issn = {1618-095X}, mesh = {Animals ; *Rheum/chemistry ; Male ; *Brain Injuries, Traumatic/drug therapy ; Mice, Inbred C57BL ; Mice ; Metagenomics ; Network Pharmacology ; Gastrointestinal Microbiome/drug effects ; Apoptosis/drug effects ; *Plant Extracts/pharmacology ; Blood-Brain Barrier/drug effects ; Disease Models, Animal ; *Drugs, Chinese Herbal/pharmacology ; Neuroprotective Agents/pharmacology ; }, abstract = {BACKGROUND: Traumatic brain injury (TBI) imposes a heavy burden on society and families owing to its high morbidity and mortality. Rhubarb has been noticed in the Chinese herb for treating TBI. The pharmacological effects include anti-inflammation, anti-bacterial, and purgative. But little is known about its potential mechanism when treating TBI.

PURPOSE: In this study, we profiled the pharmacological and intestinal functional characteristics of rhubarb in post-TBI mice.

METHODS: Fifty adult male C57BL/6 mice were randomly allocated into five groups, including sham, controlled cortical impact (CCI), and rhubarb extract administered at low, medium, and high doses. The impaired neurobehavioral function was assessed using the modified neurological severity score (mNSS) and the wire hang test. hematoxylin-eosin (HE) and Nissl staining, terminal deoxynucleotidyl transferase-mediated dUTP-nick-end labeling (TUNEL) and immunoglobulin-γ (IgG) staining, immunostaining for GFAP, TNF-α and IL-1β were applied to detect the histological damage, neuronal apoptosis and blood-brain barrier (BBB) permeability, respectively. Subsequently, the network pharmacology approaches was used to identify putative therapeutic targets and the relevant pathway of rhubarb on TBI. In addition, metagenomics and targeted metabolomics revealed the alterations in composition and functions of gut flora and gut-derived serum short-chain fatty acids (SCFAs). Finally, we depleted the gut microbiota with an antibiotic cocktail (ampicillin, metronidazole, neomycin, vancomycin) to uncover the critical role of gut microbiota on rhubarb function.

RESULTS: Rhubarb reduced brain IgG leakage and neuronal apoptosis after TBI. The network pharmacology analysis identified seven genes as key potential therapeutic targets of rhubarb, and the genes were related to inflammation, oxidant and apoptosis. The enrichment analysis showed that three of the top signal pathways were involved in anti-inflammation, anti-apoptosis and anti-oxidant. The metagenomics analysis showed that rhubarb reshaped the structure and abundance of gut microbiota in TBI. The altered function of gut microbiota was enriched in the improvement of carbohydrate metabolism, gut-derived serum SCFAs and microbial resistance. Finally, gut microbiota depletion confirmed the effects of rhubarb on post-TBI IgG leakage and neuronal apoptosis were depended on gut microbiota.

CONCLUSIONS: Rhubarb may treat TBI by effects of targeting inflammatory factors and oxidant factors to inhibit neuronal apoptosis and protect the BBB. The therapeutic effects of rhubarb are partly mediated by altering gut microbiota. Our findings not only highlight a holistic and microbial potential of rhubarb's therapeutic functional actions but also elucidate previously unrecognized therapeutic development of novel targets and strategies for TBI therapies by rhubarb.}, } @article {pmid40468430, year = {2025}, author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE}, title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {60}, pmid = {40468430}, issn = {2524-6372}, support = {#2014/21772-4 and #2014/14935-4//São Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Fundação Agrisus/ ; }, abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.

RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.

CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.}, } @article {pmid40468269, year = {2025}, author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T}, title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {154}, pmid = {40468269}, issn = {1741-7007}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; }, abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.

RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.

CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.}, } @article {pmid40468214, year = {2025}, author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D}, title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {761}, pmid = {40468214}, issn = {1471-2229}, support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; }, mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; }, abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.

RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p < 0.05).

CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.}, } @article {pmid40467587, year = {2025}, author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y}, title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5186}, pmid = {40467587}, issn = {2041-1723}, support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; }, abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.}, } @article {pmid40467356, year = {2025}, author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A}, title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.}, journal = {Revista Argentina de microbiologia}, volume = {57}, number = {3}, pages = {275-287}, doi = {10.1016/j.ram.2025.04.002}, pmid = {40467356}, issn = {0325-7541}, mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology ; Tunisia ; Female ; *Metagenomics ; Case-Control Studies ; Adult ; Male ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Young Adult ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.}, } @article {pmid40467244, year = {2025}, author = {Li, S and Rao, C and Zang, X and Yang, Y and Yang, W and Huang, X and Li, J and Sun, J and Liu, Y and Ye, D}, title = {Characterization of aroma active compounds and microbial communities in spontaneously fermented Vitis quinquangularis wines.}, journal = {Food research international (Ottawa, Ont.)}, volume = {214}, number = {}, pages = {116676}, doi = {10.1016/j.foodres.2025.116676}, pmid = {40467244}, issn = {1873-7145}, mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Vitis/microbiology/chemistry ; *Odorants/analysis ; *Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; *Microbiota ; *Food Microbiology ; }, abstract = {This study comprehensively investigated volatile compounds and microbial communities of spontaneously fermented Vitis quinquangularis wines from the Guangxi production regions. The aroma profiles of V. quinquangularis wines were analyzed by GC-O-MS, GC-QQQ-MS/MS, and quantitative descriptive analysis. The wines exhibit predominantly fruity and floral notes, with contributions from esters and (E)-β-damascenone. A distinctive and typical "green and earthy" aroma was observed, with contributions from C6 compounds and volatile phenols such as 1-hexanol, (E)-3-hexen-1-ol, hexanoic acid, 4-vinylguaiacol, eugenol, and isoeugenol. Metagenomics and culturomics analyses indicated that the dominant strains involved in the spontaneous fermentation process were Hanseniaspora opuntiae, Saccharomyces cerevisiae, Paenibacillus sp., Sphingomonas sp., and Bacillus sp. Additionally, microorganisms from sixteen generas, including Actinomycetospora and Ameyamaea, etc., along with six enzymes like EC 1.1.1.1 and EC 1.1.1.318, etc., were implicated in the production of the "green and earthy" aroma in V. quinquangularis wines.}, } @article {pmid40467108, year = {2025}, author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N}, title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.}, journal = {Journal of clinical periodontology}, volume = {52}, number = {7}, pages = {999-1010}, pmid = {40467108}, issn = {1600-051X}, support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; /ERC_/European Research Council/International ; }, mesh = {Humans ; *Peri-Implantitis/microbiology/diagnosis ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; Cross-Sectional Studies ; Female ; *Microbiota/genetics ; Middle Aged ; Biomarkers/analysis ; *Dental Implants/microbiology ; Aged ; Adult ; Machine Learning ; Mucositis/microbiology ; Stomatitis/microbiology ; }, abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.

MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.

RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p ≤ 0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p < 0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score ≥ 2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC = 0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC = 0.79-0.87).

CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.}, } @article {pmid40467013, year = {2025}, author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S}, title = {Targeted analysis of metagenomes: divide and conquer.}, journal = {Biotechnology advances}, volume = {83}, number = {}, pages = {108619}, doi = {10.1016/j.biotechadv.2025.108619}, pmid = {40467013}, issn = {1873-1899}, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targeted methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.}, } @article {pmid40467000, year = {2025}, author = {Potrykus, M and Kurpas, M and Gałęzowska, G and Gajewska, M}, title = {Linking chemical contamination to composition of bacterial communities in urban beach sands of a brackish sea under anthropogenic pressure.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {381}, number = {}, pages = {126596}, doi = {10.1016/j.envpol.2025.126596}, pmid = {40467000}, issn = {1873-6424}, mesh = {*Environmental Monitoring ; *Bathing Beaches ; *Bacteria/classification ; *Sand/chemistry ; *Water Pollutants, Chemical/analysis ; Seawater/microbiology/chemistry ; Polycyclic Aromatic Hydrocarbons/analysis ; Microbiota ; RNA, Ribosomal, 16S ; Biodiversity ; }, abstract = {The water quality on recreational beaches is constantly monitored. However, given that beachgoers often spend more time in contact with the sand than the seawater, it is essential to also regularly assess beach sand quality. In this study, 34 beach sand samples were collected in seven locations along the south shore of the Baltic Sea (Europe) between 2022 and 2023. The samples were obtained from recreational beaches with significant anthropogenic pressure. Since the use of new chemicals is widespread, it is imperative to not only monitor known contaminants but also to actively search for the presence of new ones in the environment. In order to establish the connection between the bacterial biodiversity and their possible resilience in the contaminated marine environment, the bacterial abundances in the beach sand were compared based on 16S rDNA sequencing with chemical contamination examined with non-targeted GC-MS. One hundred forty-nine (149) distinct chemicals were detected, many of which are of human health concern. The presence of polycyclic aromatic hydrocarbons, plasticizers and benzothiazoles in the sand samples was observed, and these contaminants were found to be associated with alterations in the bacterial community structure, characterized by a decrease or increase in certain taxonomic groups. Notably, the bacterial communities exhibited specificity to each location and demonstrated stability throughout the seasons. Furthermore, the presence of DNA from 31 potential human pathogens was detected in the sand. These findings emphasize the necessity for regular monitoring of beach sand for the presence of toxic chemicals and pathogens to safeguard public health and the environment.}, } @article {pmid40465720, year = {2025}, author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK}, title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.}, journal = {Science advances}, volume = {11}, number = {23}, pages = {eadt1466}, pmid = {40465720}, issn = {2375-2548}, mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; }, abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.}, } @article {pmid40465264, year = {2025}, author = {Liu, M and Geng, J and Jin, S and Hu, P and Wang, X and Liu, X}, title = {Alterations of the Enteric Virome in Vogt-Koyanagi-Harada Disease.}, journal = {Investigative ophthalmology & visual science}, volume = {66}, number = {6}, pages = {15}, pmid = {40465264}, issn = {1552-5783}, mesh = {Humans ; *Uveomeningoencephalitic Syndrome/virology/microbiology ; Male ; Female ; *Virome/genetics ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria/genetics ; Metagenomics ; Young Adult ; }, abstract = {PURPOSE: This study aims to explore the enteric virome characteristics of Vogt Koyanagi Harada (VKH) disease and its potential role in this disease.

METHODS: Shotgun metagenomic sequencing was used to detect the enteric virome and 16S rRNA to detect the bacteriome in new-onset, untreated patients with VKH (n = 25) and age- and sex-matched healthy controls without autoimmune diseases (n = 25).

RESULTS: Patients with VKH exhibited different enteric viral communities from healthy controls, characterized by decreased richness of core viral communities (present in > 80% of samples) and increased richness of common viral communities (present in 50%-80% of samples). Notably, within the core virus community, bacteriophage richness was markedly reduced, whereas eukaryotic virus richness significantly increased in patients with VKH. The case-control analysis identified 42 differentially abundant viruses, including a decrease in crAss-like phages, the eukaryotic virus Moumouvirus_moumou, and an enrichment of the Chlamydiamicrovirus_CPG1. Most of the differential phages predominantly targeted bacteria from the phyla Pseudomonadota and Firmicutes. The gut virome-bacteria community correlation analysis revealed a shift in the interactions between the core viruses and bacterial communities. Additionally, Wroclawvirus PA5oct (a Pseudomonas phage) correlated with leukotrichia, a clinically relevant symptom of VKH (P = 0.042). The impact of multiple Pseudomonas phages on the host folate biosynthesis was significantly enhanced in patients with VKH. Moreover, the protein (Earp361-372) encoded by VKH-enriched Pseudomonas was identified to share homology with the melanin antigen gp10044-59.

CONCLUSIONS: The gut virome of patients with VKH differs significantly from healthy controls, suggesting its disturbance may contribute to gut microbiome imbalance and VKH development.}, } @article {pmid40464558, year = {2025}, author = {Ruan, Y and Zhu, T and Yang, R and Su, F and An, C and Hu, Z and Li, X and Li, Y and Chen, P and Shao, X and Qin, J and Chen, H and Chen, R}, title = {Donor-derived microbial engraftment and gut microbiota shifts associated with weight loss following fecal microbiota transplantation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {7}, pages = {e0012025}, pmid = {40464558}, issn = {1098-5336}, support = {82100860//National Natural Science Foundation of China/ ; 82370864//National Natural Science Foundation of China/ ; 2019A1515110658//Natural Science Foundation of Guangdong Province/ ; 2024A04J4869//Science and Technology Program of Guangzhou/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/therapy ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Obesity/therapy/microbiology ; Overweight/therapy/microbiology ; Tissue Donors ; *Weight Loss ; }, abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis and may provide metabolic benefits for obesity. However, its mechanisms and variability in clinical outcomes remain poorly understood. This 12-week multicenter, single-arm study evaluated the efficacy of FMT for weight loss and explored the role of donor-derived microbial engraftment and functional shifts in mediating weight loss among overweight and obese individuals. Twenty-three participants (body mass index ≥24 kg/m[2]) without diabetes received three biweekly FMT sessions via a nasojejunal tube. Fecal samples from participants and donors were analyzed using metagenomic sequencing. By week 12, 52% of participants were classified as responders, achieving significant weight loss of ≥5% from baseline, with an average weight loss of 7.98 ± 2.69 kg (P < 0.001). In contrast, non-responders lost 2.90 ± 1.89 kg (P < 0.001). Responders exhibited a significantly higher proportion of donor-derived microbial strains post-FMT compared to non-responders (37.8% vs 15.2%, P = 0.020). Notably, key taxa, including Phascolarctobacterium (P = 0.034) and Acidaminococcaceae (P = 0.012), increased significantly in abundance in responders post-FMT, indicating successful microbial engraftment as a critical determinant of therapeutic success. These findings suggest that FMT is a viable intervention for weight loss in obese individuals. Successful donor-derived microbial engraftment strongly correlates with weight loss efficacy, highlighting the potential of microbiota-targeted therapies in obesity management and providing insights into the mechanisms underlying FMT outcomes.IMPORTANCEPrior research indicates that fecal microbiota transplantation (FMT) is a promising treatment for diseases related to microbiota imbalance, potentially providing metabolic benefits for obesity. However, the specific role of donor-derived microbial engraftment in driving clinical efficacy has remained unclear. In this study, we evaluated the efficacy of FMT in promoting weight loss and explored the role of donor-derived bacterial strains in this process. Our findings demonstrate that the successful engraftment of specific donor-derived taxa, such as Phascolarctobacterium and Acidaminococcaceae, is strongly associated with significant weight loss. This highlights the critical interplay between donor microbiota and recipient gut environment. These findings underscore the potential of microbiota-targeted therapies as a novel strategy for obesity management.CLINICAL TRIALSThis study is registered with the Chinese Clinical Trial Registry as ChiCTR1900024760.}, } @article {pmid40463374, year = {2025}, author = {Gu, J and Ma, Y and Chang, Q and Chen, L}, title = {Influence of programmed death ligand 1 (PD-L1) knockout on gut microbiota in experimental autoimmune uveitis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1600673}, pmid = {40463374}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Uveitis/immunology/microbiology/genetics ; *B7-H1 Antigen/genetics/deficiency ; *Autoimmune Diseases/immunology/microbiology/genetics ; Mice, Knockout ; Mice ; Female ; Disease Models, Animal ; Mice, Inbred C57BL ; }, abstract = {PURPOSE: Programmed death ligand 1 (PD-L1) is a potential target for autoimmune disease therapies. The gut microbiota plays a critical role in autoimmunity, and may influence therapeutic outcomes of immune therapies in cancer. However, the relationship between PD-L1 and gut microbiota in autoimmune conditions remains unclear. This study aims to investigate the effect of PD-L1 knockout on gut microbiota in an experimental autoimmune uveitis (EAU) model.

METHODS: EAU was induced via immunization with interphotoreceptor retinoid-binding protein peptide 651-670 (IRBP651-670) in either wild type (WT) or PD-L1 knockout (KO) C57BL/6J female mice. Sham adjuvant was administered to WT or PD-L1 KO mice as healthy controls. The severity of EAU was evaluated through clinical evaluation and histopathological gradings. The characteristics of gut microbiota was analyzed using metagenomic sequencing.

RESULTS: Each group consisted of three biological replicates. The clinical and histopathological scores of EAU were significantly higher in KO_EAU mice than in WT_EAU mice. WT_EAU mice exhibited lower microbial richness than their healthy controls (WT mice), while PD-L1 KO in EAU mice (KO_EAU group) led to increased richness when compared to wild type EAU mice (WT_EAU group). EAU induced a reduction in the abundance of Akkermansia muciniphila A and an increased in CAG-485 sp002362485. PD-L1 knockout in EAU led to an increased abundance of families Bacteroidaceae, Lachnospiraceae and Ruminococcaceae. EAU was associated with declining microbial tryptophan metabolism and up-regulated functions related to lipid and carbohydrate metabolism; PD-L1 knockout in EAU further increased the metabolism of glycan and biosynthesis of 3-deoxy-α-D-manno-2-octulosonate (Kdo), a key component of bacterial lipopolysaccharide (LPS).

CONCLUSION: Both EAU and PD-L1 knockout modulate gut microbiota, affecting microbial composition - particularly Akkermansia, CAG-485, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae - and microbial functions such as lipid, carbohydrate and glycan metabolism.}, } @article {pmid40462511, year = {2025}, author = {Qian, LM and Wang, SX and Zhou, W and Qin, ZX and Wang, YN and Zhao, Q and Xu, RH}, title = {Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, pmid = {40462511}, issn = {1477-4054}, support = {Y-HR2020QN-0474//Beijing Xisike Clinical Oncology Research Foundation/ ; 84000-31630002//Sun Yat-sen University clinical research 5010 program/ ; CIRP-SYSUCC-0004//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; 2019-I2M-5-036//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 82173128//National Natural Science Foundation of China/ ; 81930065//National Natural Science Foundation of China/ ; 82321003//National Natural Science Foundation of China/ ; }, mesh = {*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Metagenome ; Dysbiosis/virology ; }, abstract = {The role of gut microbiota, especially viruses, in colorectal cancer (CRC) pathogenesis remains unclear. This study investigated the interplay between gut microbiota and CRC development. We developed a viral/bacterial sequence analysis pipeline to reanalyze gut metagenomic datasets from eight CRC studies. A multisample co-occurrence network was constructed to delineate microbiota species interconnections. Our analysis confirmed dysbiosis in CRC patients and revealed enrichment of viral species, particularly those hosted by Lactococcus and Escherichia. These viruses were identified as central hubs in the multikingdom interaction network. We developed a network-based model using single sample networks (SSN) that distinguished CRC patients from controls with an area under the curve (AUC) of 0.93. Models combining relative abundance and SSN assessment achieved an AUC of 0.97, outperforming SSN-based models without viral data. This study highlights the crucial role of viruses in the gut microbiome network and their potential as targets for CRC prevention and intervention. Our approach offers a new perspective on noninvasive diagnostic criteria for CRC.}, } @article {pmid40462354, year = {2025}, author = {Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, JE and Weisgerber, DW and Modavi, C and Turnbaugh, PJ and Abate, AR}, title = {Microbiome Single Cell Atlases Generated with a Commercial Instrument.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {27}, pages = {e2409338}, pmid = {40462354}, issn = {2198-3844}, support = {U01AI129206//Foundation for the National Institutes of Health/ ; R01 HG008978/HG/NHGRI NIH HHS/United States ; R01 AT011117/AT/NCCIH NIH HHS/United States ; R01EB019453//Foundation for the National Institutes of Health/ ; COA7000-138420-7030928-45-A73H5//UCSF Benioff Center for Microbiome Medicine (BCMM) Trainee Pilot Award/ ; R01 AI149699/AI/NIAID NIH HHS/United States ; R01 EB019453/EB/NIBIB NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; F32GM140808//Foundation for the National Institutes of Health/ ; F32 GM140808/GM/NIGMS NIH HHS/United States ; R01AT011117//Foundation for the National Institutes of Health/ ; U01 AI129206/AI/NIAID NIH HHS/United States ; //Florida State University Start-up fund/ ; R01HG008978//Foundation for the National Institutes of Health/ ; R01AI149699//Foundation for the National Institutes of Health/ ; R01HL122593//Foundation for the National Institutes of Health/ ; }, mesh = {*Single-Cell Analysis/methods/instrumentation ; *Microbiota/genetics ; Humans ; Computational Biology/methods ; Metagenomics/methods ; }, abstract = {Single-cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single-cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, EASi-seq (Easily Accessible Single microbe sequencing) is presented. By adapting the single-cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbial genomes. EASi-seq allows tens of thousands of microbes to be sequenced per run and, as it is shown, can generate detailed atlases of human and environmental microbiomes. The ability to capture large genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, a companion bioinformatic pipeline is developed that clusters genome by sequence similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, the integration of metagenomic contigs with the EASi-seq datasets is demonstrated to reduce capture bias and increase coverage. EASi-seq enables high-quality single-cell genomic sequencing for microbiome samples using a simple workflow run on a commercially available platform.}, } @article {pmid40462165, year = {2025}, author = {Gao, H and Bai, H and Su, Y and Gao, Y and Fang, H and Li, D and Yu, Y and Lu, X and Xia, D and Mao, D and Luo, Y}, title = {Fecal microbiota transplantation from Helicobacter pylori carriers following bismuth quadruple therapy exacerbates alcohol-related liver disease in mice via LPS-induced activation of hepatic TLR4/NF-κB/NLRP3 signaling.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {627}, pmid = {40462165}, issn = {1479-5876}, support = {42377426//National Natural Science Foundation of China/ ; 42077382//National Natural Science Foundation of China/ ; 21JCYBJC01200//Tianjin Municipal Natural Science Foundation/ ; 2023220//Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Helicobacter pylori/physiology/drug effects ; *Signal Transduction/drug effects ; Lipopolysaccharides/pharmacology ; *Bismuth/therapeutic use/pharmacology ; *Toll-Like Receptor 4/metabolism ; Gastrointestinal Microbiome/drug effects ; *NF-kappa B/metabolism ; *Liver/pathology/metabolism/drug effects ; *Liver Diseases, Alcoholic/microbiology/therapy/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Helicobacter Infections/microbiology ; Disease Models, Animal ; Humans ; Dysbiosis ; }, abstract = {BACKGROUND: Helicobacter pylori infection is common in patients with alcohol-related liver disease (ALD), and bismuth quadruple therapy (BQT) is widely used for eradication. However, its impact on ALD remains unclear. This study aims to characterize BQT-induced gut microbiota alterations in asymptomatic H. pylori carriers and evaluate their effect on an ALD mouse model.

METHODS: Metagenomic sequencing was conducted to assess the gut microbiota composition of individuals before and after BQT. Fecal microbiota transplantation (FMT) from these donors was performed in an ALD mouse model. Gut microbiota in mice was analyzed by 16S rRNA sequencing. Liver and intestinal parameters were assessed using western blot, RT-qPCR, histopathology, ELISA, and flow cytometry.

RESULTS: BQT treatment significantly altered the gut microbiota in H. pylori carriers, increasing the abundance of opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, Klebsiella quasipneumoniae, and Klebsiella variicola, while decreasing beneficial bacteria such as Bifidobacterium, Eubacterium, Bacteroides, Faecalibacterium, and Blautia. In ALD mice receiving FMT from post-BQT donors, exacerbated gut dysbiosis was observed, marked by an enrichment of Enterobacteriaceae and Escherichia-Shigella. These microbiota changes were associated with impairment of intestinal barrier integrity, as evidenced by reduced levels of mucins, tight junction proteins, and antimicrobial peptides, along with a decrease in Treg cells and an increase in Th17 and Th1 cells. Additionally, this dysbiosis led to elevated serum lipopolysaccharide (LPS) levels, which activated the hepatic NLRP3 inflammasome pathway and subsequently increased IL-18 and IL-1β levels. Furthermore, liver function and oxidative stress markers, including ALT, AST, MDA, GSSG/GSH ratio, and SOD, were significantly elevated, indicating severe liver dysfunction and increased oxidative stress. Finally, probiotic supplementation effectively mitigated the negative effects of BQT-induced gut microbiota remodeling on ALD in mice.

CONCLUSIONS: BQT markedly alters the gut microbiota in H. pylori carriers, promoting dysbiosis that exacerbates ALD in mice via LPS-mediated activation of hepatic inflammatory pathways. These findings highlight the need for careful consideration of BQT use in ALD patients.}, } @article {pmid40462041, year = {2025}, author = {Luo, Y and Wu, R and Wu, W and Zhao, D and Jiang, Y and Gu, H}, title = {Differences in pulmonary microbiota of severe community-acquired pneumonia with different pathogenic microorganisms in children.}, journal = {BMC pediatrics}, volume = {25}, number = {1}, pages = {449}, pmid = {40462041}, issn = {1471-2431}, support = {82200008//the Youth Program of National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Community-Acquired Infections/microbiology ; Male ; Female ; Child, Preschool ; Haemophilus influenzae/isolation & purification ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; *Lung/microbiology ; Streptococcus pneumoniae/isolation & purification ; Mycoplasma pneumoniae/isolation & purification ; *Pneumonia, Bacterial/microbiology ; Child ; Severity of Illness Index ; Pneumonia, Mycoplasma/microbiology ; C-Reactive Protein/analysis ; Community-Acquired Pneumonia ; }, abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is the leading cause of hospitalization and death in children under 5 years old. Recently, the number of children with severe CAP (SCAP) has increased significantly, and local or systemic complications may occur. However, changes in the pulmonary microbiota of SCAP with different pathogens and their relationship with the clinical features of SCAP remain unclear.

METHODS: This study collected bronchoalveolar lavage fluid (BALF) from 105 children with SCAP for metagenomics next generation sequencing (mNGS). According to the first pathogen of mNGS, the enrolled children were divided into the Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP) and Haemophilus influenzae (HI) groups. We aimed to explore differences in clinical features and pulmonary microbiota of SCAP with different pathogens, and clarify the correlation between pulmonary microbiota and clinical features.

RESULTS: Fever days and the levels of C-reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), D-dimer and heparin-binding protein (HBP) of children in MP group were significantly higher than those in HI group. The level of LDH of children in MP group was significantly higher than that in SP group. The abundance of MP was also positively correlated with fever days and the levels of PCT, LDH and D-dimer. The α diversity of SP group was significantly increased compared to MP group and HI group.

CONCLUSION: Compared to SP-infected and HI-infected children with SCAP, children with SCAP infected with MP tend to have a more intense inflammatory response. The α diversity was higher in the lower airways of children with SCAP and SP infections compared to MP-infected and HI-infected children with SCAP.}, } @article {pmid40461820, year = {2025}, author = {Piccinno, G and Thompson, KN and Manghi, P and Ghazi, AR and Thomas, AM and Blanco-Míguez, A and Asnicar, F and Mladenovic, K and Pinto, F and Armanini, F and Punčochář, M and Piperni, E and Heidrich, V and Fackelmann, G and Ferrero, G and Tarallo, S and Nguyen, LH and Yan, Y and Keles, NA and Tuna, BG and Vymetalkova, V and Trompetto, M and Liska, V and Hucl, T and Vodicka, P and Bencsiková, B and Čarnogurská, M and Popovici, V and Marmorino, F and Cremolini, C and Pardini, B and Cordero, F and Song, M and Chan, AT and Derosa, L and Zitvogel, L and Huttenhower, C and Naccarati, A and Budinska, E and Segata, N}, title = {Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer.}, journal = {Nature medicine}, volume = {31}, number = {7}, pages = {2416-2429}, pmid = {40461820}, issn = {1546-170X}, support = {CGCATF-2023/100041//Cancer Research UK (CRUK)/ ; U01 CA176726/CA/NCI NIH HHS/United States ; OT2 CA297205/CA/NCI NIH HHS/United States ; 825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1OT2CA297205-01//U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; R35 CA253185/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; 101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; OT2 CA297680/CA/NCI NIH HHS/United States ; U01 CA261961/CA/NCI NIH HHS/United States ; R01 CA263776/CA/NCI NIH HHS/United States ; CGCATF-2023/100036//Cancer Research UK (CRUK)/ ; OT2CA297680//U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/genetics/diagnosis ; *Feces/microbiology ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Biomarkers, Tumor/genetics ; Metagenomics/methods ; Fusobacterium nucleatum/genetics ; Middle Aged ; Cohort Studies ; Aged ; Adenoma/microbiology/pathology/genetics ; Ruminococcus/genetics ; Faecalibacterium prausnitzii/genetics ; }, abstract = {Associations between the gut microbiome and colorectal cancer (CRC) have been uncovered, but larger and more diverse studies are needed to assess their potential clinical use. We expanded upon 12 metagenomic datasets of patients with CRC (n = 930), adenomas (n = 210) and healthy control individuals (n = 976; total n = 2,116) with 6 new cohorts (n = 1,625) providing granular information on cancer stage and the anatomic location of tumors. We improved CRC prediction accuracy based solely on gut metagenomics (average area under the curve = 0.85) and highlighted the contribution of 19 newly profiled species and distinct Fusobacterium nucleatum clades. Specific gut species distinguish left-sided versus right-sided CRC (area under the curve = 0.66) with an enrichment of oral-typical microbes. We identified strain-specific CRC signatures with the commensal Ruminococcus bicirculans and Faecalibacterium prausnitzii showing subclades associated with late-stage CRC. Our analysis confirms that the microbiome can be a clinical target for CRC screening and characterizes it as a biomarker for CRC progression.}, } @article {pmid40460917, year = {2025}, author = {Lian, ZH and You, Z and Han, PY and Qiu, Y and Zhang, YZ and Ge, XY}, title = {Decoding the virome reveals diverse novel viruses in tree shrews (Tupaia belangeri) in Yunnan Province.}, journal = {Virologica Sinica}, volume = {40}, number = {3}, pages = {314-323}, pmid = {40460917}, issn = {1995-820X}, mesh = {Animals ; *Virome/genetics ; China ; Phylogeny ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Metagenomics ; *Tupaia/virology ; }, abstract = {Viruses circulating in small mammals possess the potential to infect humans. Tree shrews are a group of small mammals inhabiting widely in forests and plantations, but studies on viruses in tree shrews are quite limited. Herein, viral metagenomic sequencing was employed to detect the virome in the tissue and swab samples from seventy-six tree shrews that we collected in Yunnan Province. As the results, genomic fragments belonging to eighteen viral families were identified, thirteen of which contain mammalian viruses. Through polymerase chain reaction (PCR) and Sanger sequencing, twelve complete genomes were determined, including five parvoviruses, three torque teno viruses (TTVs), two adenoviruses, one pneumovirus, and one hepacivirus, together with three partial genomes, including two hepatitis E viruses and one paramyxovirus. Notably, the three TTVs, named TSTTV-HNU1, TSTTV-HNU2, and TSTTV-HNU3, may compose a new genus within the family Anelloviridae. Notably, TSParvoV-HNU5, one of the tree shrew parvoviruses detected, was likely to be a recombination of two murine viruses. Divergence time estimation further revealed the potential cross-species-transmission history of the tree shrew pneumovirus TSPneV-HNU1. Our study provides a comprehensive exploration of viral diversity in wild tree shrews, significantly enhancing our understanding of their roles as natural virus reservoirs.}, } @article {pmid40460542, year = {2025}, author = {Smirnova, AV and Verbeke, TJ and Furgason, CC and Albakistani, EA and Nwosu, FC and Kim, JJ and Haupt, ES and Sheremet, A and Lee, ES and Trang, E and Richardson, E and Dacks, JB and Dunfield, PF}, title = {Microbial community development in an oil sands pit lake.}, journal = {The Science of the total environment}, volume = {987}, number = {}, pages = {179764}, doi = {10.1016/j.scitotenv.2025.179764}, pmid = {40460542}, issn = {1879-1026}, mesh = {*Lakes/microbiology ; *Microbiota ; *Oil and Gas Fields ; Mining ; *Environmental Monitoring ; RNA, Ribosomal, 16S/analysis ; *Water Microbiology ; Canada ; Bacteria ; }, abstract = {Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.}, } @article {pmid40460541, year = {2025}, author = {Kang, MG and Kwak, MJ and Kang, A and Park, J and Lee, DJ and Mun, J and Kim, S and Mun, D and Lee, W and Choi, H and Seo, E and Choi, Y and Jeong, KC and Oh, S and Kim, J and Kim, Y}, title = {Metagenome-based microbial metabolic strategies to mitigate ruminal methane emissions using Komagataeibacter-based symbiotics.}, journal = {The Science of the total environment}, volume = {987}, number = {}, pages = {179793}, doi = {10.1016/j.scitotenv.2025.179793}, pmid = {40460541}, issn = {1879-1026}, mesh = {Animals ; *Methane/metabolism ; *Rumen/microbiology/metabolism ; *Metagenome ; Cattle ; Symbiosis ; Fermentation ; *Gastrointestinal Microbiome ; }, abstract = {Global warming increasingly threatens organisms in equatorial regions, where temperatures often exceed physiological limits. Rumen methanogens are a major biological source of anthropogenic methane, a potent greenhouse gas. Therefore, ruminal methane mitigation strategies that preserve animal productivity are urgently needed. Our In vitro analysis of Holstein steer rumen fluid-integrating gas production, volatile fatty acid (VFA) profiles, and metagenomic data-demonstrated that kombucha, a fermented beverage, effectively reduces methane emissions by modulating ruminal fermentation. Rumen fluid was incubated for 60 h under three treatments (control, 3-NOP, and kombucha). During the initial 30 h, kombucha reduced methane by 15.07 % compared to the control but was 17.54 % higher than 3-NOP. In the subsequent 30 h, kombucha achieved sustained reductions of 34.72 % versus the control and 26.28 % versus 3-NOP, highlighting its uniquely sustained methane-reducing effect. A metagenomics-guided screening and in vitro validation identified Komagataeibacter intermedius SLAM-NK6B as a key strain underlying the methane-reducing effect of kombucha. The genome of SLAM-NK6B encodes biosynthetic gene clusters for cellulose, malate, citrate, and methanobactin-metabolites that can modulate the rumen microbiota. SLAM-NK6B supplementation reduced methanogen abundance by 53.32 % and increased hydrogen pressure, shifting microbial metabolism. Excluding acetate, VFA production increased significantly, with propionate levels elevated by 15.39-43.81 %. Metagenomic data further indicated activation of alternative hydrogen sink pathways, including citrate-to-propionate and malate-to-propionate conversions. This study proposes a novel microbial metabolic strategy for methane mitigation, enabling both methane reduction and enhanced fermentation efficiency. Such metabolic guidance of the rumen microbiome offers a sustainable approach to low-emission ruminant production.}, } @article {pmid40459709, year = {2025}, author = {Quoc, NB and Nhu, LTT and Chau, NNB}, title = {Identification of diet resources of big-eyed bug Geocoris ochropterus (Fieber) (Hemiptera: Geocoridae) by multiplex PCR and shotgun metagenomic approaches.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {537}, pmid = {40459709}, issn = {1573-4978}, support = {E2022.02.1//Đại học Mở Thành phố Hồ Chí Minh/ ; }, mesh = {Animals ; *Metagenomics/methods ; Multiplex Polymerase Chain Reaction/methods ; *Hemiptera/genetics ; Diet ; Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; }, abstract = {BACKGROUND: Big-eyed bugs (Geocoris spp.) are important generalist predators in agricultural ecosystems, playing a crucial role in natural pest control.

METHODS: To better understand their dietary sources, we assessed the plant and animal food sources in the gut of Geocoris ochropterus using multiplex PCR and shotgun metagenomic analysis. The PCR assays targeted genetic markers from both animal (COI) and plant (matK and rbcL) DNA.

RESULTS: Results revealed the presence of both animal and plant-derived DNA in the gut samples, indicating that Geocoris ochropterus feeds on a mixed diet. Additionally, the results of shotgun metagenomic sequencing of the gut microbiota showed a predominance of Eukaryota, with over 80% of sequences belonging to this domain, while a diverse range of taxonomic groups were identified, including arthropods, plants, bacteria, and fungi. Arthropods particularly insects from the orders Lepidoptera, Hemiptera, Hymenoptera, Coleoptera, Phasmatodea and plants belonging to the orders Brassicales, Cucurbitales, and Poales constituted the most abundant dietary components. At the genus level, notable taxa included Maniola (family Nymphalidae), Carposina (Carposinidae), Helicoverpa (Noctuidae), and Solanum (Solanaceae). Species-level analysis confirmed the dominance of several insect species, including Maniola hyperanthus, Carposina sasakii, and Bombyx mori, alongside plant species such as Cucumis melo, Gossypium hirsutum, and Digitaria exilis.

CONCLUSIONS: These findings provide a comprehensive characterization of the diet of Geocoris ochropterus, highlighting its role as a generalist predator with a diverse diet consisting of both insect and plant food sources. This study contributes to the understanding of Geocoris ochropterus as a potential biocontrol agent in agricultural systems.}, } @article {pmid40456950, year = {2025}, author = {Kocharovskaya, Y and Delegan, Y and Sevostianov, S and Bogun, A and Demin, DV}, title = {Metagenomic Analysis of Pulp and Paper Wastes and Prospects for Their Self-purification.}, journal = {Current microbiology}, volume = {82}, number = {7}, pages = {320}, pmid = {40456950}, issn = {1432-0991}, mesh = {*Paper ; *Metagenomics ; Lignin/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Industrial Waste/analysis ; Biodegradation, Environmental ; *Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {Thousands of tons of waste accumulate, as a result of the activities of the pulp and paper industry, which is often stored in the form of dumps. However, intensifying the use of lignocellulose for more efficient bioremediation remains highly challenging. Therefore, the study of microbiomes with potentially desirable characteristics for the decomposition of pulp and paper wastes is currently an important task. In this study, a comprehensive assessment of the microbiota biodiversity of these dumps was carried out using high-throughput, high-resolution sequencing. In study 472 million high-quality clean reads assembled into 6,413,337 contigs with a total length of 4306 Mb, of which 3,633,174 open reading frames (ORFs) were identified. The core microbiome was composed of four phyla from Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Representatives of phylum Proteobacteria prevailed in samples. Annotation using the KEGG database in the Metabolism category resulted in 654,234 ORFs and 5138 ORFs encoding enzymes/proteins involved in degradation of lignocellulose which formed main pool of the wastes. By use of the created database, the search for lignocellulose degradation genes showed that genera Shewanella, Achromobacter, and Delftia covered significant part of the reads. The results indicate that the established microbiome of local landfills can be considered as an important source for improving lignocellulose bioremediation, provided that lignocellulosic fungi are sufficiently active. In whole, these new data can be used as a scientific basis to form an efficient eco-biotechnology for auto-remediation of pulp and paper industry waste.}, } @article {pmid40456770, year = {2025}, author = {Zhou, XQ and Chen, KH and Yu, RQ and Yang, M and Liu, Q and Hao, YY and Li, J and Liu, HW and Feng, J and Tan, W and Huang, Q and Gu, B and Liu, YR}, title = {Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5102}, pmid = {40456770}, issn = {2041-1723}, support = {42425701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methylmercury Compounds/metabolism/toxicity ; *Oryza/metabolism/microbiology ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; }, abstract = {Toxic methylmercury (CH3Hg[+]) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg[+] degradation, the identities of microbes and pathways accountable for CH3Hg[+] degradation in soil remain elusive. Here, we combine [13]CH3Hg[+]-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg[+] degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of [13]CH3Hg[+] in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg[+] in pure culture assays. Metagenomic analysis further reveals that most of these candidate [13]CH3Hg[+] degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg[+] reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg[+] contributes to 0.08-0.64 fold decreases in CH3Hg[+] accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62-13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg[+] degradation in soil, with potential implications for development of bioremediation strategies.}, } @article {pmid40456384, year = {2025}, author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P}, title = {Gut and oral microbial profile associations to oral cancer.}, journal = {Journal of dentistry}, volume = {160}, number = {}, pages = {105848}, doi = {10.1016/j.jdent.2025.105848}, pmid = {40456384}, issn = {1879-176X}, mesh = {Humans ; *Mouth Neoplasms/microbiology/pathology ; Saliva/microbiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; Aged ; *Microbiota ; *Gastrointestinal Microbiome ; Adult ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor/analysis ; }, abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n = 30) divided into three groups based on histology; Benign (B) (n = 15), Potentially Malignant (PM) (n = 8), and Malignant (M) (n = 7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.}, } @article {pmid40454811, year = {2025}, author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM}, title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.}, journal = {mBio}, volume = {16}, number = {7}, pages = {e0110825}, pmid = {40454811}, issn = {2150-7511}, support = {P20GM146584, P20GM139769/NH/NIH HHS/United States ; U19 AI090871/AI/NIAID NIH HHS/United States ; P20 GM146584/GM/NIGMS NIH HHS/United States ; K01-DK111794/NH/NIH HHS/United States ; AI124255, AI090871/NH/NIH HHS/United States ; K01 DK111794/DK/NIDDK NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; R35 GM150609/GM/NIGMS NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; Mice ; *Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; Male ; Metagenomics ; Metabolomics ; }, abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.

IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.}, } @article {pmid40454480, year = {2025}, author = {Lynch, LE and Lahowetz, R and Maresso, C and Terwilliger, A and Pizzini, J and Melendez Hebib, V and Britton, RA and Maresso, AW and Preidis, GA}, title = {Present and future of microbiome-targeting therapeutics.}, journal = {The Journal of clinical investigation}, volume = {135}, number = {11}, pages = {}, pmid = {40454480}, issn = {1558-8238}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Phage Therapy/trends/methods ; Bacteriophages ; Animals ; }, abstract = {A large body of evidence suggests that single- and multiple-strain probiotics and synbiotics could have roles in the management of specific gastrointestinal disorders. However, ongoing concerns regarding the quality and heterogeneity of the clinical data, safety in vulnerable populations, and the lack of regulation of products containing live microbes are barriers to widespread clinical use. Safety and regulatory issues must be addressed and new technologies considered. One alternative future strategy is the use of synthetic bacterial communities, defined as manually assembled consortia of two or more bacteria originally derived from the human gastrointestinal tract. Synthetic bacterial communities can model functional, ecological, and structural aspects of native communities within the gastrointestinal tract, occupying varying nutritional niches and providing the host with a stable, robust, and diverse gut microbiota that can prevent pathobiont colonization by way of colonization resistance. Alternatively, phage therapy is the use of lytic phage to treat bacterial infections. The rise of antimicrobial resistance has led to renewed interest in phage therapy, and the high specificity of phages for their hosts has spurred interest in using phage-based approaches to precisely modulate the microbiome. In this Review, we consider the present and future of microbiome-targeting therapies, with a special focus on early-life applications, such as prevention of necrotizing enterocolitis.}, } @article {pmid40452057, year = {2025}, author = {Francioli, D and Kampouris, ID and Kuhl-Nagel, T and Babin, D and Sommermann, L and Behr, JH and Chowdhury, SP and Zrenner, R and Moradtalab, N and Schloter, M and Geistlinger, J and Ludewig, U and Neumann, G and Smalla, K and Grosch, R}, title = {Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {148}, pmid = {40452057}, issn = {1474-760X}, support = {031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Zea mays/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Stress, Physiological ; Bacillus ; Plant Roots/microbiology ; Soil Microbiology ; *Agricultural Inoculants/physiology ; }, abstract = {BACKGROUND: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits.

RESULTS: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores.

CONCLUSIONS: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.}, } @article {pmid40451466, year = {2025}, author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P}, title = {Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions.}, journal = {Genomics}, volume = {117}, number = {4}, pages = {111064}, doi = {10.1016/j.ygeno.2025.111064}, pmid = {40451466}, issn = {1089-8646}, mesh = {*Phaseolus/microbiology/genetics ; *Microbiota ; *Host-Pathogen Interactions ; Bacteria/genetics/classification ; }, abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3-5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels-spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species-both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of "Replication, recombination, and repair" processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.}, } @article {pmid40451005, year = {2025}, author = {Su, X and Liu, J and Chang, L and Hu, W and Fang, Y and Li, J and Huang, L and Shu, W and Dong, H}, title = {Viral insights into the acidification of sulfidic mine tailings.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138754}, doi = {10.1016/j.jhazmat.2025.138754}, pmid = {40451005}, issn = {1873-3336}, mesh = {*Mining ; Hydrogen-Ion Concentration ; Genome, Viral ; Sulfur/metabolism ; Metals, Heavy/analysis ; *Viruses/genetics ; Iron/metabolism ; Bacteria/genetics/metabolism ; Metagenome ; }, abstract = {The acidification of sulfidic mine tailings, driven primarily by sulfur- and iron-oxidizing microorganisms, can lead to severe environmental pollution and imperil human health. The role of viruses in this process and its underlying mechanisms yet remain poorly understood. In this study, we recovered 623 species-level viral genomes and 322 prokaryotic genomes from seven metagenomes of mine tailings with pH values ranging from 7.51 to 2.13. We observed that acidification drastically altered geochemical properties and degraded environmental quality, characterized by significant decreases in carbon/nitrogen ratio and heavy metal levels. The structure and function of viral communities were significantly correlated with pH and prokaryotic diversity, showing distinct dynamics across different acidification stages, similar to patterns observed in the prokaryotic community. Notably, potential sulfur-oxidizing prokaryotes increased in relative abundance as pH declined, while their virus-host abundance ratio exhibited a significant positive correlation with pH. Results indicated that viral "top-down" predation on sulfur-oxidizing prokaryotes was likely suppressed during acidification, providing a survival advantage to these organisms over iron-oxidizing counterparts. Moreover, viruses likely reprogrammed the sulfur and iron metabolism of prokaryotic hosts and enhanced their adaptability to environmental stressors through auxiliary metabolic genes. Additionally, a pH- and lifestyle-dependent evolutionary scenario for viruses revealed that frequent recombination and the accumulation of synonymous mutations in lytic viruses and chronic Inoviridae, likely increased their intrapopulation diversity and resilience. These findings provide new insights into the multifaceted roles of viruses in mine tailings acidification, deepening understanding of the underlying mechanisms and advancing potential strategies to mitigate associated environmental risks.}, } @article {pmid40450783, year = {2025}, author = {Rajput, V and Pramanik, R and Nannaware, K and Shah, P and Bhalerao, A and Jain, N and Shashidhara, LS and Kamble, S and Dastager, S and Dharne, M}, title = {Metagenomics based longitudinal monitoring of antibiotic resistome and microbiome in the inlets of wastewater treatment plants in an Indian megacity.}, journal = {The Science of the total environment}, volume = {986}, number = {}, pages = {179691}, doi = {10.1016/j.scitotenv.2025.179691}, pmid = {40450783}, issn = {1879-1026}, mesh = {India ; *Wastewater/microbiology ; *Microbiota ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; *Environmental Monitoring ; Bacteria ; Waste Disposal, Fluid ; Cities ; }, abstract = {The growing threat of antimicrobial resistance (AMR) poses a significant global challenge, undermining advancements in healthcare, agriculture, and life expectancy. Despite its critical importance, data on population-level AMR trends, including seasonal and temporal variations, remain scarce. In this study, we conducted metagenomic analysis on 190 wastewater samples collected monthly from December 2022 to December 2023 in Pune, India, to assess the diversity, dynamics, and co-occurrence of AMR determinants. Using nanopore shotgun sequencing, we generated 87.86 Gbp of data, enabling the taxonomic classification of 157 bacterial phyla and 3291 genera. Proteobacteria dominated the microbial community, with notable seasonal shifts, including increased Streptococcus abundance correlating with SARS-CoV-2 viral surges in March 2023. We identified 637 distinct antimicrobial resistance genes (ARGs) associated with 29 antibiotic classes, with multidrug, macrolide-lincosamide-streptogramin, beta-lactams, and tetracyclines genes being the most prevalent, particularly within WHO priority pathogens such as Enterobacteriaceae and Pseudomonas. Temporal normalization of ARG abundance revealed significant seasonal variability, peaking during winter, potentially driven by increased antibiotic use for respiratory infections. The integration of viral load data with AMR trends highlighted complex interactions between viral outbreaks and AMR dissemination. This study demonstrates the potential of wastewater surveillance as an early warning system for AMR, providing valuable insights into environmental and community resistance dynamics. Our results underscore the importance of integrated AMR surveillance to inform public health strategies aimed at mitigating the global AMR threat.}, } @article {pmid40450182, year = {2025}, author = {Wang, C and Dong, T and Rong, X and Yang, Y and Mou, J and Li, J and Ge, J and Mu, X and Jiang, J}, title = {Microbiome in prostate cancer: pathogenic mechanisms, multi-omics diagnostics, and synergistic therapies.}, journal = {Journal of cancer research and clinical oncology}, volume = {151}, number = {6}, pages = {178}, pmid = {40450182}, issn = {1432-1335}, support = {82172230//the National Natural Science Foundation of China/ ; 21ZGY29//the Changchun Scientific and Technological Development Program/ ; 3R218FM83430//Life Spring AKY Pharmaceuticals/ ; 20240205001YY//the Jilin Scientific and Technological Development Program/ ; 2017F014//the Jilin Health Service Capacity Improvement Program/ ; }, mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology ; Male ; *Microbiota ; Metagenomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related deaths in men, with the microbiome emerging as a significant factor in its development and progression. Understanding the microbiome's role could provide new insights into PCa pathogenesis and treatment.

OBJECTIVE: This review aims to explore the interactions between the microbiome and PCa, focusing on microbial imbalances and their effects on immune responses, inflammation, and hormone levels. It also discusses advanced research techniques and the potential for microbiome modulation in PCa management.

METHODS: The review synthesizes current literature on the microbiome's role in PCa, highlighting differences in microbial composition between cancerous and healthy prostate tissues. It examines techniques such as high-throughput sequencing and metagenomics and explores the mechanisms through which the microbiome influences PCa.

CONCLUSIONS: The review reveals substantial microbial differences in prostate tissues of PCa patients compared to healthy individuals, indicating a potential link between microbiome alterations and disease progression. It highlights the promise of microbiome-based strategies for diagnosis and treatment and underscores the need for further research into personalized, microbiome-centric approaches for PCa management.}, } @article {pmid40449763, year = {2025}, author = {Liu, W and Chen, S and Yang, J and Chen, Y and Yang, Q and Lu, L and Li, J and Yang, T and Zhang, G and Hu, J}, title = {Characterization of blood and urine microbiome temporal variability in patients with acute myeloid leukemia.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107734}, doi = {10.1016/j.micpath.2025.107734}, pmid = {40449763}, issn = {1096-1208}, mesh = {Humans ; *Leukemia, Myeloid, Acute/microbiology/blood/urine ; Male ; Middle Aged ; Female ; *Microbiota ; Longitudinal Studies ; Aged ; Adult ; *Urine/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; *Blood/microbiology ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.

METHODS: We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.

RESULTS: The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.

CONCLUSION: This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.}, } @article {pmid40449445, year = {2025}, author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F}, title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {125972}, doi = {10.1016/j.jenvman.2025.125972}, pmid = {40449445}, issn = {1095-8630}, mesh = {*Denitrification ; *Bioreactors ; Biofilms ; Carbon/metabolism ; Nitrogen/metabolism ; Wastewater ; Metagenomics ; Microbiota ; Waste Disposal, Fluid ; }, abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.}, } @article {pmid40448586, year = {2025}, author = {Jones, LM and El Aidy, S}, title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40448586}, issn = {1751-7370}, support = {ENPPS.IPP.019.004/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Biofilms/growth & development ; Corrosion ; Oxidation-Reduction ; *Ecosystem ; Bacteria/metabolism ; Electron Transport ; Host Microbial Interactions ; }, abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between electroactive microorganisms (EAM)-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.}, } @article {pmid40448221, year = {2025}, author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF}, title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.}, journal = {Alzheimer's research & therapy}, volume = {17}, number = {1}, pages = {122}, pmid = {40448221}, issn = {1758-9193}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; }, abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.

METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.

RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.

CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.}, } @article {pmid40447596, year = {2025}, author = {Wang, X and Jiang, Q and Tian, X and Chen, W and Mai, J and Lin, G and Huo, Y and Zheng, H and Yan, D and Wang, X and Li, T and Gao, Y and Mou, X and Zhao, W}, title = {Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {92}, pmid = {40447596}, issn = {2055-5008}, mesh = {Adult ; Female ; Humans ; Pregnancy ; Young Adult ; Biofilms/growth & development ; China ; Gardnerella vaginalis/growth & development ; *Lactobacillus/genetics/isolation & purification/classification/physiology ; *Metagenomics/methods ; Microbiota ; Pregnant People ; *Vagina/microbiology ; Vaginosis, Bacterial/microbiology ; }, abstract = {This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.}, } @article {pmid40447574, year = {2025}, author = {Rodríguez Del Río, Á and Scheu, S and Rillig, MC}, title = {Soil microbial responses to multiple global change factors as assessed by metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5058}, pmid = {40447574}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects ; Metagenome ; Soil/chemistry ; Droughts ; Microbiota/genetics ; Salinity ; *Climate Change ; Global Warming ; }, abstract = {Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.}, } @article {pmid40445833, year = {2025}, author = {Li, W and Huang, B and Guo, M and Zeng, Z and Cai, T and Feng, L and Zhang, X and Guo, L and Jiang, X and Yin, Y and Wang, E and Huang, X and Zheng, J}, title = {Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework.}, journal = {Cell reports}, volume = {44}, number = {6}, pages = {115773}, doi = {10.1016/j.celrep.2025.115773}, pmid = {40445833}, issn = {2211-1247}, mesh = {*Antimicrobial Peptides/genetics/chemistry/pharmacology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance poses a major threat to public health, prompting the development of alternative therapies such as antimicrobial peptides (AMPs). Protein language models (PLMs) have advanced protein structure and function predictions, facilitating AMP discovery. We developed antimicrobial peptide structural evolution miner (AMP-SEMiner), an AI-driven framework that integrates PLMs, structural clustering, and evolutionary analysis to systematically identify AMPs encoded by small open reading frames and AMP-containing proteins in metagenome-assembled genomes. AMP-SEMiner identified over 1.6 million AMP candidates across diverse environments. Experimental validation showed antimicrobial activity in 9 of the 20 tested candidates, with 5 surpassing antibiotic effectiveness; variant peptides derived from these candidates similarly demonstrated strong antimicrobial efficacy. AMPs from human gut microbiomes revealed both conserved and adaptive evolutionary strategies, reflecting their dynamic ecological roles. AMP-SEMiner thus represents a valuable tool for expanding AMP discovery and has significant potential to inform the development of alternative antimicrobial treatments.}, } @article {pmid40445192, year = {2025}, author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL}, title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {40445192}, issn = {2050-084X}, support = {CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; R01 AI139154/AI/NIAID NIH HHS/United States ; AI139154/NH/NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; 2330095//National Science Foundation/ ; }, mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; }, abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.}, } @article {pmid40443669, year = {2025}, author = {Zhang, C and Xu, Y and Zhang, M and Li, J and Sun, Z and Wang, Y and Lin, P}, title = {An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1500866}, pmid = {40443669}, issn = {1664-3224}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/immunology/microbiology/metabolism ; Adult ; Proteomics/methods ; *Th2 Cells/immunology/metabolism ; *Th1 Cells/immunology/metabolism ; Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; *Pregnancy Complications/immunology/metabolism/microbiology ; *Proteome ; Cytokines/metabolism ; }, abstract = {OBJECTIVE: To explore the gut microbiota and proteomic characteristics of hypothyroidism in the first half of pregnancy (referred to as hypothyroidism in the first half of pregnancy) and its association with Th (T helper cells, Th)1/Th2 balance using metagenomics combined with proteomics.

METHODS: Stool and blood samples were collected from 20 hypothyroid (hypothyroidism group) and normal pregnant women (normal group) in the first half of pregnancy. Flora and proteomic characteristics were analyzed using metagenomics sequencing and 4D-DIA proteomics. Th1 and Th2 cells were quantified, and cytokine levels were measured using cellular micro-bead arra. The enzyme-linked immunosorbent test (ELISA) was utilized to assess differential proteins.

RESULTS: (1) Metagenomic sequencing revealed distinct microbial profiles: The β-diversity of gut microbiota was diminished in the hypothyroidism group (p < 0.05). LEfSe analysis identified Phocaeicola vulgatus and Bacteroides fragilis enriched in the hypothyroidism group (p<0.05), and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed significant enrichment in pathways related to peptidoglycan biosynthesis and glycerol ester metabolism.(2) Proteomic analysis demonstrated downregulation of Diacylglycerol Kinase Kappa (DGKK) and P05109|S10A8(S10A8) proteins in the hypothyroidism group, with marked enrichment in the KEGG pathways for vascular smooth muscle contraction and phosphatidylinositol signaling. (3) ELISA validation confirmed that the proteins DGKK and S10A8 were downregulated in pregnant women in the hypothyroidism group.

CONCLUSION: Increased P. vulgatus and B. fragilis, decreased DGKK and S10A8 proteins, and a left shift in the Th1/Th2 balance in patients with hypothyroidism in the first half of pregnancy may be associated with the development of the disease.}, } @article {pmid40442718, year = {2025}, author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P}, title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.}, journal = {International breastfeeding journal}, volume = {20}, number = {1}, pages = {44}, pmid = {40442718}, issn = {1746-4358}, support = {LM2023069//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 857560//Horizon 2020 Framework Programme/ ; }, mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation & purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs & derivatives ; }, abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.

METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24 h, 48 h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.

RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+ PMA) were significantly lower than in untreated (-PMA) samples (p < 0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p < 0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48 h (p > 0.05). Of specific genera, only + PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p < 0.05) in comparison to + PMA fresh human milk samples.

CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4 °C for up to 48 h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.}, } @article {pmid40442154, year = {2025}, author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ}, title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {91}, pmid = {40442154}, issn = {2055-5008}, mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation & purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation & purification ; Transcriptome ; Multiomics ; }, abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.}, } @article {pmid40441146, year = {2025}, author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B}, title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.}, journal = {Cell host & microbe}, volume = {33}, number = {6}, pages = {957-972.e6}, pmid = {40441146}, issn = {1934-6069}, support = {I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; U01 AA021856/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Virulence Factors/genetics/antagonists & inhibitors/metabolism ; Mice ; *Escherichia coli/genetics/pathogenicity/drug effects/metabolism ; *Liver Diseases, Alcoholic/microbiology/drug therapy ; Gastrointestinal Microbiome ; Disease Models, Animal ; Feces/microbiology ; Kupffer Cells/metabolism/microbiology ; *Escherichia coli Proteins/genetics/metabolism/antagonists & inhibitors ; Male ; Female ; Liver/pathology/microbiology ; Germ-Free Life ; Ethanol ; Mice, Inbred C57BL ; Escherichia coli Infections/microbiology ; Bacterial Capsules/metabolism ; Hepatitis, Alcoholic/microbiology ; }, abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.}, } @article {pmid40440092, year = {2025}, author = {Lawniczak, MKN and Kocot, KM and Astrin, JJ and Blaxter, M and Sotero-Caio, CG and Barker, KB and Childers, AK and Coddington, J and Davis, P and Howe, K and Johnson, WE and McKenna, DD and Wideman, JG and Pettersson, OV and Ras, V and Santos, BF and , }, title = {Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40440092}, issn = {2047-217X}, support = {//Science for Life Laboratory/ ; //Swedish Research Council/ ; 1846174//National Science Foundation/ ; 2138994//National Science Foundation/ ; 2321308//National Science Foundation/ ; 2001303//National Science Foundation/ ; 2110053//National Science Foundation/ ; 1937815//National Science Foundation/ ; DBI-2119963//National Science Foundation/ ; U24HG006941/HG/NHGRI NIH HHS/United States ; /NH/NIH HHS/United States ; //Agricultural Research Service/ ; }, mesh = {*Genome ; *Genomics/standards/methods ; *Metagenomics/standards/methods ; Earth, Planet ; *Specimen Handling/standards/methods ; }, abstract = {The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.}, } @article {pmid40439232, year = {2025}, author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC}, title = {Polyphenol rewiring of the microbiome reduces methane emissions.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40439232}, issn = {1751-7370}, mesh = {*Methane/metabolism ; *Microbiota/drug effects ; *Catechin/metabolism ; *Polyphenols/metabolism ; Hydrogen/metabolism ; *Bacteria/metabolism/genetics/classification ; Greenhouse Gases/metabolism ; Soil Microbiology ; }, abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, ~40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72%-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from Days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.}, } @article {pmid40438118, year = {2025}, author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M}, title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1561459}, pmid = {40438118}, issn = {1664-3224}, support = {D43 CA260658/CA/NCI NIH HHS/United States ; D43 TW010543/TW/FIC NIH HHS/United States ; R21 AI148033/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; }, abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.

METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.

FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.

CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.}, } @article {pmid40437611, year = {2025}, author = {Zhang, P and Tuo, X and Jiang, J and Zhang, Y and Zhao, J and Deng, C and Zhao, G and Cheng, Y and Song, L and Yang, Y and Guo, R and Zhang, H and Zhao, H and Ma, S and Li, L and Shi, H}, title = {Characteristics of the gut virome in patients with premalignant colorectal adenoma.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {597}, pmid = {40437611}, issn = {1479-5876}, support = {No.S2024-JC-QN-1554//Natural Science Basic Research Program of Shaanxi Province/ ; }, mesh = {Humans ; *Virome ; *Colorectal Neoplasms/virology/microbiology ; *Adenoma/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Precancerous Conditions/virology/microbiology ; Case-Control Studies ; Aged ; Reproducibility of Results ; }, abstract = {BACKGROUND: The multi-kingdom gut microbiota (e.g., bacteriome, mycobiome, and virome) characteristics of colorectal cancer have been extensively studied, yet there is still an insufficient description of the microbiota features in its early-stage, colorectal adenoma, particularly in the gut virome aspect.

METHODS: Based on the Metagenomic Gut Virus catalogue (MGV) containing 54,118 non-redundant gut viral genomes, this study characterized the virome composition and diversity using publicly available metagenomic sequencing data from 419 individuals with premalignant colorectal adenoma and 552 healthy controls. Furthermore, we identified and assessed the reliability and classification performance of adenoma-associated microbial signatures through comparative analysis and the random forest model.

RESULTS: Our results revealed a notable shift in the gut virome structure of patients compared to healthy controls, characterized by a significant increase in viral families such as Microviridae, Podoviridae_crAss-like, and Quimbyviridae. At the viral operational taxonomic unit (vOTU) level, we identified 479 vOTU signatures showing significant differences in relative abundances between patients and controls, including some patient-enriched vOTUs tending to infect Bacteroidaceae and Lachnospiraceae. Correlation network analysis revealed specific bacterial species correlated with adenoma-associated viruses, suggesting frequent interactions between them. Moreover, random forest models trained on gut viral and bacterial signatures demonstrated area under the curve (AUC) scores of 0.68, 0.82, and 0.76 for classifying healthy individuals versus patients with tubular adenomas, patients with sessile serrated adenomas, and patients with both conditions, respectively. In three independent validation cohorts, the classification performance achieved AUC scores ranging from 0.61 to 0.65.

CONCLUSIONS: Our study provides insights into the gut virome in premalignant colorectal adenoma, highlighting its potential role in disease development and diagnosis. Further investigations are warranted to elucidate the underlying mechanisms of gut virus-bacteria interactions and validate diagnostic models in larger populations.}, } @article {pmid40436871, year = {2025}, author = {Zeng, L and Yu, B and Zeng, P and Duoji, Z and Zuo, H and Lian, J and Yang, T and Dai, Y and Feng, Y and Yu, P and Yang, J and Yang, S and Dou, Q}, title = {Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {90}, pmid = {40436871}, issn = {2055-5008}, support = {723B2017//National Natural Science Foundation of China/ ; XZ202201ZD0001G//Science and Technology Major Project of Tibetan Autonomous Region of China/ ; XZ202303ZY0007G//Science and Technology Plan Projects of Tibet Autonomous Region/ ; CQFYJB01005//Chongqing Maternal and Child Health Hospital/ ; 2023YFC3604702//National Key Research and Development Program of China/ ; 2023YFC3604701; 2020YFC2008005; 2018YFC2002405//National Key Research and Development Program of China/ ; 2023YFS0251//Key R&D Project of Sichuan Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dyslipidemias/microbiology/epidemiology ; Male ; Cross-Sectional Studies ; Female ; *Life Style ; Middle Aged ; Adult ; *Metabolic Networks and Pathways ; Feces/microbiology/chemistry ; China ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Metabolomics ; Triglycerides/blood ; Aged ; }, abstract = {Whether the role of gut microbial features lies in the pathways from lifestyles to dyslipidemia remains unclear. In this cross-sectional study, we conducted a metagenome-wide association analysis and fecal metabolomic profiling in 994 adults from the China Multi-Ethnic cohort. A total of 26 microbial species were identified as mediators between lifestyle factors and risk for dyslipidemia. Specifically, the abundance of [Ruminococcus] gnavus mediated the associations between lifestyles and risks for dyslipidemia, elevated low-density lipoprotein cholesterol, elevated total cholesterol, and elevated triglycerides. [Ruminococcus] gnavus, Alistipes shahii, and Lachnospira eligens were replicated to be associated with dyslipidemia in an external validation cohort. The potential metabolic pathways included arachidonic acid, bile acid, and aromatic amino-acid metabolism.}, } @article {pmid40436643, year = {2025}, author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y}, title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.}, journal = {Journal of Zhejiang University. Science. B}, volume = {26}, number = {5}, pages = {477-492}, pmid = {40436643}, issn = {1862-1783}, support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; }, mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; }, abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.}, } @article {pmid40436373, year = {2025}, author = {Vosough, M and Drees, F and Sieber, G and Stach, TL and Beisser, D and Probst, AJ and Boenigk, J and Schmidt, TC}, title = {Integrative Analysis of Nontargeted LC-HRMS and High-Throughput Metabarcoding Data for Aquatic Environmental Studies Using Combined Multivariate Statistical Approaches.}, journal = {Analytical chemistry}, volume = {97}, number = {22}, pages = {11563-11571}, pmid = {40436373}, issn = {1520-6882}, mesh = {Chromatography, Liquid ; Mass Spectrometry ; Multivariate Analysis ; Wastewater/chemistry/analysis ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; *High-Throughput Screening Assays ; *DNA Barcoding, Taxonomic ; }, abstract = {Significant progress in high-throughput analytical techniques has paved the way for novel approaches to integrating data sets from different compartments. This study leverages nontarget screening (NTS) via liquid chromatography-high-resolution mass spectrometry (LC-HRMS), a crucial technique for analyzing organic micropollutants and their transformation products, in combination with biological indicators. We propose a combined multivariate data processing framework that integrates LC-HRMS-based NTS data with other high-throughput data sets, exemplified here by 18S V9 rRNA and full-length 16S rRNA gene metabarcoding data sets. The power of data fusion is demonstrated by systematically evaluating the impact of treated wastewater (TWW) over time on an aquatic ecosystem through a controlled mesocosm experiment. Highly compressed NTS data were compiled through the implementation of the region of interest-multivariate curve resolution-alternating least-squares (MCR-ALS) method, known as ROIMCR. By integrating ANOVA-simultaneous component analysis with structural learning and integrative decomposition (SLIDE), the innovative SLIDE-ASCA approach enables the decomposition of global and partial common, as well as distinct variation sources arising from experimental factors and their possible interactions. SLIDE-ASCA results indicate that temporal variability explains a much larger portion of the variance (74.6%) than the treatment effect, with both contributing to global shared space variation (41%). Design structure benefits include enhanced interpretability, improved detection of key features, and a more accurate representation of complex interactions between chemical and biological data. This approach offers a greater understanding of the natural and wastewater-influenced temporal patterns for each data source, as well as reveals associations between chemical and biological markers in an exemplified perturbed aquatic ecosystem.}, } @article {pmid40435904, year = {2025}, author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H}, title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116925}, doi = {10.1016/j.diagmicrobio.2025.116925}, pmid = {40435904}, issn = {1879-0070}, mesh = {Humans ; *Appendicitis/microbiology/pathology ; Child ; Male ; Female ; Child, Preschool ; Adolescent ; *Bacteria/classification/isolation & purification/genetics ; Acute Disease ; Severity of Illness Index ; C-Reactive Protein/analysis ; *Microbiota ; Appendectomy ; Metagenomics ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.

METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.

RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.

CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.}, } @article {pmid40435563, year = {2025}, author = {García-Pérez, P and Tomas, M and Giuberti, G and Capanoglu, E and Callegari, ML and Lucini, L and Patrone, V}, title = {Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128226}, doi = {10.1016/j.micres.2025.128226}, pmid = {40435563}, issn = {1618-0623}, mesh = {*Gastrointestinal Microbiome/physiology ; *Brassica/metabolism/chemistry ; Fermentation ; Humans ; *Digestion ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Intestine, Large/microbiology/metabolism ; Metabolomics ; Metagenomics ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Polyphenols/metabolism ; Metabolome ; Isothiocyanates/metabolism ; Multiomics ; }, abstract = {Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.}, } @article {pmid40434915, year = {2025}, author = {Kuntz, TM and Liu, L and Wang, K and Everett, C and Eliassen, AH and Willett, WC and Sinha, R and Chan, AT and Rimm, EB and Garrett, WS and Segata, N and Piccinno, G and Huttenhower, C and Morgan, X and Song, M}, title = {Comparing the Metagenomic Performance of Stools Collected from Custom Cards and 95% Ethanol in Epidemiologic Studies.}, journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {34}, number = {8}, pages = {1368-1376}, pmid = {40434915}, issn = {1538-7755}, support = {R01CA263776//National Institutes of Health (NIH)/ ; U01CA176726//National Institutes of Health (NIH)/ ; U01 CA176726/CA/NCI NIH HHS/United States ; U01CA261961//National Institutes of Health (NIH)/ ; R35CA253185//National Institutes of Health (NIH)/ ; R35 CA253185/CA/NCI NIH HHS/United States ; U01 CA261961/CA/NCI NIH HHS/United States ; R01 CA263776/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; Female ; *Ethanol ; Middle Aged ; Male ; *Colorectal Neoplasms/microbiology/epidemiology ; *Specimen Handling/methods ; *Gastrointestinal Microbiome/genetics ; Epidemiologic Studies ; Adult ; }, abstract = {BACKGROUND: Stool cards have been used for microbiome assessment in epidemiologic studies.

METHODS: We compared shotgun metagenomic sequencing from 32 participants who self-collected stool samples from the same bowel movement using a custom stool card versus a collection tube with 95% ethanol fixative in the Nurses' Health Study II. We evaluated the agreement between methods at both the whole-community and individual species levels. To contextualize the comparison for disease association studies, we assessed the performance of the two collection methods for differentiating colorectal cancer-associated taxa.

RESULTS: Overall, metagenomes from cards and 95% ethanol were highly correlated within individuals. No difference was found in α diversity and only ∼1% of variation in β diversity was explained by the collection method. At the species level, although the relative abundances were highly correlated between card and ethanol sample pairs (Spearman rho = 0.96), 10 (of 239) species showed a differential abundance in paired samples, including overrepresentation of Escherichia coli and underrepresentation of three Streptococcus species in cards compared with ethanol. Among a set of 99 colorectal cancer-associated species, four showed differential abundances between collection methods; however, this number was consistent with that expected by chance.

CONCLUSIONS: Metagenomic sequencing using stool samples self-collected using stool cards or 95% ethanol yielded largely consistent results although differential abundances were observed for a small number of individual species.

IMPACT: Stool cards can be a cost-effective alternative to collect stool samples for metagenomic sequencing in epidemiologic studies but warrant additional considerations for data analysis.}, } @article {pmid40434822, year = {2025}, author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM}, title = {From air to insight: the evolution of airborne DNA sequencing technologies.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {5}, pages = {}, pmid = {40434822}, issn = {1465-2080}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation & purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; }, abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.}, } @article {pmid40434093, year = {2025}, author = {Koldaş, SS and Sezerman, OU and Timuçin, E}, title = {Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0019625}, pmid = {40434093}, issn = {2379-5077}, mesh = {*Cystic Fibrosis/microbiology/physiopathology ; Humans ; *Microbiota/genetics ; Sputum/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Lung/physiopathology/microbiology ; }, abstract = {UNLABELLED: Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.

IMPORTANCE: Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.}, } @article {pmid40434078, year = {2025}, author = {Weisse, L and Martin, L and Moumen, B and Héchard, Y and Delafont, V}, title = {Environmental diversity of Candidatus Babelota and their relationships with protists.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0026125}, pmid = {40434078}, issn = {2379-5077}, support = {ANR-21-CE02-0001//Agence Nationale de la Recherche/ ; }, mesh = {*Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; *Eukaryota/genetics/classification ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Ca. Babelota is a phylum of strictly intracellular bacteria whose representatives are commonly detected in various environments through metagenomics, though their presence, ecology, and biology have never been addressed so far. As a group of strict intracellular, we hypothesize that their presence, occurrence, and abundance heavily depend on their hosts, which are known as heterotrophic protists, based on few described isolates. Here, we conducted a sampling campaign allowing to characterize protists and associated bacterial communities, using high-throughput sequencing. In parallel, a systematic enrichment of protists from samples was performed to attempt characterization and isolation of new Ca. Babelota within native hosts. We found that Ca. Babelota are among the most widespread phylum among the rare ones. Protist enrichments are allowed in certain cases to enrich as well for Ca. Babelota, which could be visualized in vivo infecting protist cells. Though cosmopolitan, Ca. Babelota diversity was highly site-specific. Cooccurrence analyses allowed to retrieve well-known as well as new putative associations involving numerous protists of various trophic regimes. The combination of approaches developed in this study enhances our understanding of Ca. Babelota ecology and biology, while paving the way for future isolation of new members of this elusive phylum, which could have huge impact on protists-and ecosystems-functioning.IMPORTANCEOur understanding of microbial diversity surrounding us and colonizing the environment has been dramatically impacted by the advent of DNA-based analyses. Such progress helped shine a new light on numerous lineages of yet-to-be-characterized microbes, whose ecology and biology are basically unknown. Among those uncharacterized clades is the Candidatus Babelota, a bacterial phylum for which parasitism seems to be an ancestral trait. All known Ca. Babelota thrive by infecting phagotrophic protist hosts, thereby impacting this basal link of the trophic chain. The Ca. Babelota constitutes a model that stands out, as phylum-wide conserved parasitism has only been described in one previous occurrence for Bacteria, with the Chlamydiota. Thus, exploring the intricate interplay between Ca. Babelota and their protist hosts will advance our knowledge of bacterial diversity, their ecology, and global impact on ecosystem functioning.}, } @article {pmid40433668, year = {2025}, author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF}, title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1531084}, pmid = {40433668}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Adult ; Biomarkers ; Aged ; }, abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.}, } @article {pmid40431358, year = {2025}, author = {Yue, Y and Yang, HJ and Li, C and Ryu, MS and Seo, JW and Jeong, DY and Park, S}, title = {Beneficial Effects of Traditional Fermented Soybean Sauce (Kanjang) on Memory Function, Body Water, and Glucose Metabolism: Roles of Gut Microbiota and Neuroinflammation.}, journal = {Nutrients}, volume = {17}, number = {10}, pages = {}, pmid = {40431358}, issn = {2072-6643}, support = {2023-3//functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Rats, Sprague-Dawley ; *Soy Foods/microbiology ; Rats ; *Memory/drug effects ; *Neuroinflammatory Diseases ; *Glucose/metabolism ; Scopolamine ; *Fermented Foods ; Water/metabolism ; Neuroprotective Agents/pharmacology ; *Glycine max ; Fermentation ; }, abstract = {Background: Traditional fermented soybean foods, acting as potential synbiotics, may help mitigate cognitive impairment associated with amnesia. This study investigated the neuroprotective effects of four kanjang (Korean fermented soy sauce) varieties and their underlying mechanisms. Methods: Male Sprague Dawley rats (n = 70) were divided into seven groups: normal control, scopolamine control, positive control (1 mg/kg bw/day of donepezil), and four scopolamine-treated groups receiving different kanjang varieties (0.5% in high-fat diet). Based on their Bacillus content, the kanjang samples were categorized as traditionally made kanjang (TMK) with high Bacillus (SS-HB), TMK with medium Bacillus (SS-MB), TMK with low Bacillus (SS-LB), and factory-made kanjang (SS-FM). Results: Scopolamine administration disrupted energy, glucose, and water metabolism and impaired memory function (p < 0.05). All kanjang treatments improved insulin sensitivity, reduced inflammation, enhanced glucose tolerance, and decreased visceral fat. SS-MB, SS-HB, and SS-FM increased skeletal muscle mass. They maintained body water homeostasis by suppressing the renin-angiotensin-aldosterone system. Kanjang treatments improved memory function, with SS-FM showing the least significant effects. The treatments reduced neuronal cell death in the hippocampal CA1 region, decreased acetylcholinesterase activity, and increased brain-derived neurotrophic factor mRNA expression. Gut microbiota analysis revealed that kanjang treatments increased Lactobacillaceae and decreased Lachnospiraceae, with SS-HB and SS-LB specifically elevating Ligilactobacillus. Metagenomic analysis demonstrated enhanced glycolysis/gluconeogenesis pathways and enhanced butanoate metabolism while reducing lipopolysaccharide biosynthesis and pro-inflammatory signaling. SS-MB and SS-LB increased intestinal goblet cell counts and the serum butyrate concentration. Conclusions: These findings suggest that kanjang consumption, particularly SS-HB and SS-LB varieties, can ameliorate memory impairment in this murine model through multiple mechanisms: metabolic improvements, enhanced neurotrophic signaling, gut microbiota modulation, and reduced neuroinflammation via gut-brain axis activation. Human clinical trials are warranted to determine if these promising neuroprotective effects translate to clinical applications.}, } @article {pmid40431158, year = {2025}, author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE}, title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431158}, issn = {2076-2607}, support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.}, } @article {pmid40431145, year = {2025}, author = {Jiang, K and Ye, L and Cao, C and Che, G and Wang, Y and Hong, Y}, title = {Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431145}, issn = {2076-2607}, support = {32360005//National Natural Science Foundation of China/ ; 2022JBQN091//Fundamental Research Funds for the Inner Mongolia Normal University/ ; 2022JBTD010//Fundamental Research Funds for the Inner Mongolia Normal University/ ; }, abstract = {Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.}, } @article {pmid40431076, year = {2025}, author = {Mendybayeva, A and Makhambetov, A and Yanin, K and Taskuzhina, A and Khusnitdinova, M and Gritsenko, D}, title = {Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {40431076}, issn = {2223-7747}, support = {BR21882269//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.}, } @article {pmid40429958, year = {2025}, author = {San-Martin, MI and Chamizo-Ampudia, A and Sanchiz, Á and Ferrero, MÁ and Martínez-Blanco, H and Rodríguez-Aparicio, LB and Navasa, N}, title = {Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.}, journal = {International journal of molecular sciences}, volume = {26}, number = {10}, pages = {}, pmid = {40429958}, issn = {1422-0067}, mesh = {Humans ; *Celiac Disease/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Animals ; Metagenomics/methods ; }, abstract = {Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.}, } @article {pmid40428846, year = {2025}, author = {Torraco, A and Di Nicolantonio, S and Cardisciani, M and Ortu, E and Pietropaoli, D and Altamura, S and Del Pinto, R}, title = {Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {5}, pages = {}, pmid = {40428846}, issn = {1648-9144}, support = {SRA-882725/CCF/CCF/United States ; }, mesh = {Humans ; Female ; *Endometriosis/microbiology/physiopathology ; *Feces/microbiology ; *Vagina/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; Dysbiosis/microbiology ; Adult ; Gastrointestinal Microbiome ; Metagenomics/methods ; }, abstract = {Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.}, } @article {pmid40428372, year = {2025}, author = {Dimitrova, L and Ilieva, Y and Gouliamova, D and Kussovski, V and Hubenov, V and Georgiev, Y and Bratanova, T and Kaleva, M and Zaharieva, MM and Najdenski, H}, title = {Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor.}, journal = {Genes}, volume = {16}, number = {5}, pages = {}, pmid = {40428372}, issn = {2073-4425}, support = {КP-06-N71/8 from 08.12.2023//National Fund for Scientific Research, Republic of Bulgaria/ ; }, mesh = {*Cellulose/metabolism ; *Bioreactors/microbiology ; Anaerobiosis ; *Microbial Consortia/genetics ; Biodegradation, Environmental ; Bacteria/genetics/isolation & purification/metabolism ; Aerobiosis ; *Bacteria, Anaerobic/genetics/isolation & purification/metabolism ; Methane/metabolism ; Biofuels ; }, abstract = {Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24-38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera-Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass.}, } @article {pmid40428326, year = {2025}, author = {Sun, YF and Han, ZX and Yao, XK and Meng, J and Ren, WL and Wang, CK and Yuan, XX and Zeng, YQ and Wang, YF and Sun, ZW and Wang, JW}, title = {Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics.}, journal = {Genes}, volume = {16}, number = {5}, pages = {}, pmid = {40428326}, issn = {2073-4425}, mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Physical Conditioning, Animal ; *Bacteria/genetics/classification/isolation & purification ; }, abstract = {Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.}, } @article {pmid40428305, year = {2025}, author = {Guo, Q and Zhang, W and Xu, C and Li, X and Wang, B and Xiong, C and Duan, W and Luo, T and Wang, W and Zhou, J}, title = {Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.}, journal = {Genes}, volume = {16}, number = {5}, pages = {}, pmid = {40428305}, issn = {2073-4425}, support = {202501AS070053//Key Project of Yunnan Basic Research Program/ ; }, mesh = {Animals ; *Elephants/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Diet ; China ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.

METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.

RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.

CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.}, } @article {pmid40427823, year = {2025}, author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG}, title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {5}, pages = {}, pmid = {40427823}, issn = {1660-4601}, support = {PTDC/CTA AMB/29586/2017//Fundação para a Ciência e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; }, mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation & purification/genetics ; }, abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.}, } @article {pmid40427639, year = {2025}, author = {DeSantis, AH and Buss, K and Coker, KM and Pasternak, BA and Chi, J and Patterson, JS and Gu, H and Jurutka, PW and Sandrin, TR}, title = {Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).}, journal = {Biomolecules}, volume = {15}, number = {5}, pages = {}, pmid = {40427639}, issn = {2218-273X}, support = {GR39923//Phoenix Children's Hospital Foundation Leadership Grant/ ; }, mesh = {Humans ; Child ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolomics/methods ; Adolescent ; *Colitis, Ulcerative/microbiology/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; Biomarkers/metabolism ; Transcriptome ; Multiomics ; }, abstract = {Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.}, } @article {pmid40426500, year = {2025}, author = {Tóth, AG and Tóth, DL and Remport, L and Tóth, I and Németh, T and Dubecz, A and Patai, ÁV and Wagenhoffer, Z and Makrai, L and Solymosi, N}, title = {A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40426500}, issn = {2079-6382}, support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020/ ; 2024-2.1.2-EKÖP-2024-00018//Ministry of Culture and Innovation of Hungary/ ; }, abstract = {Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human-pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine.}, } @article {pmid40426336, year = {2025}, author = {Wang, Y and Zhou, K and Zhang, Y and Li, C and Zhang, Y and Ren, X and Mi, C and Ma, L and Duan, Y and Liu, M and Ping, G and Tian, X and Song, Z}, title = {The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens.}, journal = {Helicobacter}, volume = {30}, number = {3}, pages = {e70047}, doi = {10.1111/hel.70047}, pmid = {40426336}, issn = {1523-5378}, support = {82170562//National Natural Science Foundation of China/ ; 7232199//Beijing Natural Science Foundation/ ; BYSYZD2023008//Key Clinical Projects of Peking University Third Hospital/ ; }, mesh = {Humans ; *Feces/microbiology ; Cross-Sectional Studies ; *Helicobacter Infections/microbiology ; Male ; Middle Aged ; Female ; *Gastric Juice/microbiology ; Adult ; *Helicobacter pylori/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation & purification ; Aged ; *Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Only one limited study on 8 H. pylori-infected patients has previously assessed the impact of H. pylori infection on the microbiome of the entire gastrointestinal tract, finding no significant effect on the bacterial composition of the lower gastrointestinal tract.

METHODS: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).

RESULTS: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces-based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.

CONCLUSIONS: This study revealed that H. pylori infection significantly influenced the diversity, composition, and metabolic functional pathway of bacteria in different parts of the digestive tract and the gastric juice. Moreover, fecal microbial composition may not fully represent the mucosal microbial composition of the gastrointestinal tract.

TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2300073419.}, } @article {pmid40424445, year = {2025}, author = {Li, W and Cai, J and Chen, G and Liu, Y and Wu, X and Bai, Y and Wu, Y and Wang, T}, title = {Microbial community succession mediated by planting patterns in the Loess Plateau, China: Implications for ecological restoration.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0324786}, pmid = {40424445}, issn = {1932-6203}, mesh = {*Soil Microbiology ; China ; Soil/chemistry ; *Microbiota ; Forests ; Ecosystem ; *Environmental Restoration and Remediation ; }, abstract = {Microbial community succession plays a key role in restoring fragile ecosystems and mitigating ecological degradation. However, the mechanisms by which vegetation restoration promotes ecological restoration and microbial community reconstruction in degraded soils remain unclear. This study utilized metagenomic high-throughput sequencing technology to analyze microbial community dynamics in soil samples collected from eight different planting patterns in the ecologically degraded areas of the Chinese Loess Plateau. The results indicated significant effects of terrain location and restorative cropping patterns on soil microbial abundance and function. In particular, soil C and N nutrient abundance was highest in mixed forest soils, and the total number of microorganisms was highest and more diverse. Therefore, through vegetation restoration, mixed forests significantly enhanced regional ecological functions. Notably, creating mixed forests with both trees and shrubs resulted in optimal ecological functions, providing a valuable direction for vegetation construction and structural optimization in the region.}, } @article {pmid40424276, year = {2025}, author = {Goldman, M and Zhao, C and Pollard, KS}, title = {Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1012277}, pmid = {40424276}, issn = {1553-7358}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Linear Models ; Metagenome/genetics ; }, abstract = {Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.}, } @article {pmid40423870, year = {2025}, author = {Zhang, M and Zhang, H and Hong, A and Huang, J and Yang, L and Long, Y and Yu, Z}, title = {Dynamic changes of dental plaque and saliva microbiota in OSCC progression.}, journal = {Clinical oral investigations}, volume = {29}, number = {6}, pages = {314}, pmid = {40423870}, issn = {1436-3771}, support = {32170071//This work was funded by the National Natural Science Foundation of China/ ; 82273466//This work was funded by the National Natural Science Foundation of China/ ; 2023ZJ1120//Hunan Provincial Science and Technology Department/ ; 2024JJ2039//Natural Science Foundation of Hunan Province/ ; 2024JJ8117//Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Saliva/microbiology ; Disease Progression ; *Dental Plaque/microbiology ; *Mouth Neoplasms/microbiology/pathology ; *Carcinoma, Squamous Cell/microbiology/pathology ; Female ; *Microbiota ; Male ; Middle Aged ; Neoplasm Staging ; Metagenomics ; }, abstract = {OBJECTIVES: To elucidate the changes in microbial composition and genomics in saliva and dental plaque during the progression of Oral Squamous Cell Carcinoma (OSCC), and to identify virulence factors and pathways associated with tumor differentiation in OSCC patients.

MATERIALS AND METHODS: Using metagenomic sequencing, 64 saliva and dental plaque samples from OSCC patients at different stages of differentiation were examined.

RESULTS: The results showed notable differences in the microbial composition and genomic profiles across ecological regions and differentiation degrees. Notably, the relative abundance of specific microbes, such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Haemophilus parainfluenzae, increased in poorly differentiated OSCC. Microbial alpha diversity in dental plaque and saliva correlates with tumor T staging. Dental plaque microbiota shows higher specialization, especially in poorly differentiated tumors. Both microbiota types become more stable with advanced T staging. Genomic analysis reveals increased virulence factors in poorly differentiated stages.Subsequently, functional pathway analysis and tracing of pathogens reveal specific microbial mechanisms in oral cancer pathogenesis. Certain oral pathogens may promote tumorigenesis by secreting factors like GAPDH (glyceraldehyde-3-phosphate dehydrogenase), GspG (a gingipain precursor), and AllS (a lysine-specific gingipain precursor).

CONCLUSIONS: OSCC progression is associated with altered microbial composition, diversity, and genomic profiles in saliva and dental plaque. Poorly differentiated stages show higher abundance of pathogens and virulence factors, implicating them in tumorigenesis.

CLINICAL RELEVANCE: Understanding the microbial and genomic changes in saliva and dental plaque during OSCC progression could aid in developing new diagnostic biomarkers and targeted therapies, potentially enhancing early detection, treatment efficacy, and patient prognosis. Maintaining oral microbiota homeostasis may also help prevent oral cancer.}, } @article {pmid40422085, year = {2025}, author = {Liu, L and Shi, J and Wang, H and Du, H and Yang, J and Wei, K and Zhou, Z and Li, M and Huang, S and Zhan, L and Li, G and Lv, Y and Shen, H and Cai, W}, title = {The characteristics of tissue microbiota in different anatomical locations and different tissue types of the colorectum in patients with colorectal cancer.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0019825}, pmid = {40422085}, issn = {2379-5077}, support = {No. WX23J03//Wuhan Municipal Health Commission/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; *Rectum/microbiology/pathology ; *Colon/microbiology/pathology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; }, abstract = {The gut microbiota is intricately associated with the onset and progression of colorectal cancer (CRC), leading to significant interest in developing prevention and treatment strategies that leverage gut microbiota. In this study, we collected 57 samples from 19 CRC patients, comprising cancerous tissue, paracancerous tissue, and normal mucosa. Utilizing metagenomic sequencing and bioinformatics analysis, we identified differences in the microbiomes and their functional characteristics across the various tissue types. The results indicated that species such as Alistipes putredinis were predominantly found in normal tissues, while Pseudomonas putida was enriched in paracancerous tissue, and Malassezia restricta was prevalent in cancerous tissues. Furthermore, the microbial functions exhibited variability among the different tissue types. Random forest analysis suggested that Moraxella osloensis may be implicated in the onset and progression of colorectal cancer. We also classified the patients into three subgroups based on the anatomical location of the colorectum: right-sided colon, left-sided colon, and rectum. The subgroup analysis revealed that the microbiota enriched in normal mucosa and paracancerous tissue varied across different anatomical sites. These findings not only elucidate the characteristics of the microbiomes in the normal mucosa, paracancerous tissue, and cancerous tissues of CRC patients, thereby providing new potential targets for clinical diagnosis and treatment, but also contribute to the existing microbiome data pertinent to CRC research.IMPORTANCEThis study provides crucial insights into the relationship between gut microbiota and colorectal cancer (CRC) by analyzing microbial communities in different tissue types and anatomical locations of CRC patients. We identified distinct microbial signatures, such as Alistipes putredinis in normal tissues and Malassezia restricta in cancerous tissues, indicating location-specific microbiomes with unique functional attributes. These findings suggest potential new biomarkers or therapeutic targets for CRC. The observed microbiota variations among right-sided colon, left-sided colon, and rectum cancers underscore the heterogeneity of CRC, pointing toward more personalized treatment strategies. By enhancing our understanding of the microbiome's role in CRC, this research paves the way for innovative diagnostic tools and targeted therapies tailored to individual patient profiles. This work is essential for advancing clinical approaches to CRC management.}, } @article {pmid40421996, year = {2025}, author = {Yang, H and Yang, Y and Cui, G and Xu, Y and Zhao, R and Le, G and Xie, Y and Li, P}, title = {Dietary methionine restriction ameliorates atherosclerosis by remodeling the gut microbiota in apolipoprotein E-knockout mice.}, journal = {Food & function}, volume = {16}, number = {12}, pages = {4904-4922}, doi = {10.1039/d5fo00841g}, pmid = {40421996}, issn = {2042-650X}, mesh = {Animals ; *Atherosclerosis/metabolism/diet therapy/microbiology ; *Gastrointestinal Microbiome ; *Methionine/metabolism/deficiency/administration & dosage ; Mice ; Male ; *Apolipoproteins E/genetics/metabolism/deficiency ; Mice, Knockout ; Mice, Inbred C57BL ; Oxidative Stress ; Diet, High-Fat/adverse effects ; Aorta/metabolism ; Mice, Knockout, ApoE ; }, abstract = {Dietary methionine restriction (MR) has been shown to reduce the risk of atherosclerosis, but the specific regulatory effects and mechanisms remain unclear. This research intends to investigate the effects of MR on atherosclerosis in apolipoprotein E-knockout (ApoE[-/-]) mice fed a high-fat, high-cholesterol, high-choline diet and their mechanisms. ApoE[-/-] mice were fed a normal diet (0.86% methionine + 4.5% fat + 0% cholesterol + 0.2% choline), a high-fat, high-cholesterol, high-choline diet (0.86% methionine + 20% fat + 1% cholesterol + 1% choline), or a high-fat, high-cholesterol, high-choline + MR diet (0.17% methionine + 20% fat + 1% cholesterol + 1% choline) for 8 consecutive weeks. The results show that MR reduced body weight, fat mass, fat deposition in the liver and adipocytes, and plasma lipid levels; improved the morphological structure of the aorta; and reduced the aortic lesion area and lipid levels. In addition, MR downregulated aortic pro-inflammatory cytokine levels, upregulated aortic anti-inflammatory cytokine levels, and improved aortic oxidative stress. Moreover, metagenomic sequencing results suggested that MR improved the gut microbiota composition, particularly through increased relative abundance of short-chain fatty acid (SCFA)-producing bacteria, and changed the relative abundance of inflammation-, lipid metabolism-, and bile acid metabolism-related bacteria at the species level. Furthermore, MR promoted SCFA production and bile acid metabolism, and reduced cell adhesion molecules and foam cell formation in the aorta. Thus, our findings indicated that MR improved the gut microbiota composition, especially increased SCFA production, and ameliorated oxidative stress and inflammation in the aorta, thereby preventing atherosclerosis.}, } @article {pmid40420833, year = {2025}, author = {Clasen, F and Yildirim, S and Arıkan, M and Garcia-Guevara, F and Hanoğlu, L and Yılmaz, NH and Şen, A and Celik, HK and Neslihan, AA and Demir, TK and Temel, Z and Mardinoglu, A and Moyes, DL and Uhlen, M and Shoaie, S}, title = {Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2506843}, pmid = {40420833}, issn = {1949-0984}, mesh = {Humans ; *Parkinson Disease/microbiology/physiopathology ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; *Brain/physiopathology/microbiology ; Male ; Female ; Aged ; *Bacteria/genetics/classification/pathogenicity/isolation & purification ; Metagenomics ; Virulence ; Virulence Factors/genetics/metabolism ; Saliva/microbiology/chemistry ; Middle Aged ; }, abstract = {The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.}, } @article {pmid40419960, year = {2025}, author = {Shen, Q and Fan, X and Sun, Y and Gao, H and Su, X}, title = {TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {136}, pmid = {40419960}, issn = {1471-2105}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 32070086//National Natural Science Foundation of China/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Algorithms ; Machine Learning ; Humans ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S-based approach often lead to profiling discrepancies, particularly at the species level, compromising the accuracy and reliability of findings.

RESULTS: To address this issue, we present TaxaCal (Taxonomic Calibrator), a machine learning algorithm designed to calibrate species-level taxonomy profiles in 16S amplicon data using a two-tier correction strategy. Validation on in-house produced and public datasets shows that TaxaCal effectively reduces biases in amplicon sequencing, mitigating discrepancies between microbial profiles derived from 16S and WGS. Moreover, TaxaCal enables seamless cross-platform comparisons between these two sequencing approaches, significantly improving disease detection in 16S-based microbiome data.

CONCLUSIONS: Therefore, TaxaCal offers a cost-effective solution for generating high-resolution microbiome species profiles that closely align with WGS results, enhancing the utility of 16S-based profiling in microbiome research. As microbiome-based diagnostics continue to evolve, TaxaCal has the potential to be a crucial tool in advancing the utility of 16S sequencing in clinical and research settings.}, } @article {pmid40419790, year = {2025}, author = {Wang, D and Duan, Y and He, L and Jiang, J and Xian, J and Yuan, K and Zhang, R and Zhang, H and Wang, J and Li, N and Huang, M and Hu, C and Lu, S and Luo, Z and Deng, T and Zhang, Z and Chen, B and Li, W}, title = {Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {804}, pmid = {40419790}, issn = {2399-3642}, support = {82102301//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology/mortality ; Male ; Female ; Metagenomics/methods ; Middle Aged ; Severity of Illness Index ; *SARS-CoV-2/genetics ; *Microbiota ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Sputum/microbiology ; Adult ; Transcriptome ; *Respiratory System/microbiology ; }, abstract = {The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.}, } @article {pmid40419614, year = {2025}, author = {Lu, W and Hua, J and Zhang, M and Yan, L and Zhao, H and Lv, X}, title = {Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen microorganisms in Dongliu buffalo.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18398}, pmid = {40419614}, issn = {2045-2322}, support = {[2021]1146//Joint Research on Improved Beef Cattle Breeds in Anhui Province/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Buffaloes/microbiology ; Female ; Male ; *Metagenomics/methods ; *Metagenome ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; Phylogeny ; *Microbiota ; }, abstract = {In this study, the composition of the rumen microbiota and its functional characteristics were investigated using a metagenomic approach in Dongliu buffalo. This study compared the rumen microbial communities of six female and four male Dongliu buffaloes of similar age, weight and lifestyle. Taxonomic analysis identified 964 genera across 52 phyla, dominated by Bacteroidota (47.54%) and Bacillota (28.20%). While alpha and beta diversity showed no sex differences (PERMANOVA P = 0.82), males exhibited higher Fibrobacter at the genus level (P = 0.02). Functional profiling revealed 429 KEGG pathways, with carbohydrate metabolism (11.17%) and amino acid metabolism (9.74%) as dominant processes. Males showed enrichment in cellulose-degrading enzymes (EC2.4.1.20, EC1.2.1.90, EC2.7.1.58) and CAZymes (GH94, GT35), while females had higher Bacteroides abundance (P = 0.01) and CAZymes like CBM47. Core cellulolytic genera (Prevotella, Ruminococcus) demonstrated male-biased GH/CBM activity, linked to enhanced fiber degradation. COG annotation highlighted carbohydrate metabolism as central, with sex-specific functional partitioning in replication (female-enriched) and secondary metabolism (male-enriched). Network analysis revealed Prevotella's dominance in CAZymeme contributions and functional specialization in lignocellulose degradation pathways, suggesting sex-driven microbial adaptation to dietary fiber utilization.}, } @article {pmid40415955, year = {2025}, author = {Guo, Y and Lin, L and Zhang, M and Yu, Y and Wang, Y and Cao, J and Li, Y and Sun, X and Guan, M and Wen, S and Wang, X and Fang, Z and Duan, W and Duan, J and Huang, T and Xia, W and Guo, S and Wei, F and Zheng, D and Huang, X}, title = {Salivary mycobiome alterations in HIV-infected MSM: dominance of Pseudogymnoascus and functional shifts across disease stages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1564891}, pmid = {40415955}, issn = {2235-2988}, mesh = {Humans ; Male ; *Saliva/microbiology ; Cross-Sectional Studies ; *HIV Infections/microbiology/complications ; *Mycobiome ; Adult ; *Homosexuality, Male ; Middle Aged ; CD4 Lymphocyte Count ; *Fungi/classification/genetics/isolation & purification ; Disease Progression ; Metagenomics ; }, abstract = {BACKGROUND: Oral health is increasingly recognized as a crucial determinant of overall health in people living with HIV/AIDS (PLWHA). Specifically, the oral mycobiome may play a pivotal role in HIV-associated oral complications. However, the fungal species involved and their potential as biomarkers for HIV-related oral conditions remain poorly understood. This study investigates salivary fungal profiles in PLWHA who have sex with men (MSM), focusing on diversity, functional shifts, and correlations with disease progression.

METHODS: A cross-sectional study included 25 MSM participants divided into five groups: HIV-negative controls (n = 5) and four HIV-positive groups stratified by CD4 count: Stage 0 (HIV RNA-positive/antibody-negative; n = 5), Stage 1 (CD4 ≥500 cells/μL; n = 5), Stage 2 (CD4 200-499 cells/μL; n = 5), and Stage 3 (CD4 <200 cells/μL or opportunistic infections; n = 5). Saliva samples were collected and analyzed using metagenomic sequencing (Illumina NovaSeq platform). Bioinformatic analyses included genome assembly (MEGAHIT), gene clustering (CD-HIT), gene abundance calculation (SOAPaligner), species annotation (BLASTP), and KEGG pathway annotation (KOBAS 2.0). Statistical analyses (Kruskal-Wallis tests, Spearman's correlation) assessed associations between fungal profiles, CD4 count, and viral loads.

RESULTS: A total of 51 fungal genera were identified, with Pseudogymnoascus being the most abundant. Functional analysis revealed 113 shared KEGG pathways, of which 69 were unique to Stage 3, primarily related to metabolic and disease-related processes. Notably, Auricularia exhibited a positive correlation with CD4 count (P ≤ 0.01), while Mucor showed a negative correlation (P = 0.0299).

CONCLUSIONS: Salivary mycobiome composition and function shift significantly across HIV stages, reflecting immune decline. Pseudogymnoascus dominance challenges conventional views of oral fungal ecology in immunocompromised hosts. These findings highlight the mycobiome's diagnostic potential for monitoring HIV-related oral health. Longitudinal studies are needed to validate clinical relevance.}, } @article {pmid40415184, year = {2025}, author = {Sheyn, U and Poff, KE and Eppley, JM and Leu, AO and Bryant, JA and Li, F and Romano, AE and Burger, A and Barone, B and DeLong, EF}, title = {Mesoscale eddies shape Prochlorococcus community structure and dynamics in the oligotrophic open ocean.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40415184}, issn = {1751-7370}, mesh = {*Prochlorococcus/genetics/classification/growth & development ; *Seawater/microbiology/chemistry ; Phylogeny ; Pacific Ocean ; Ecosystem ; Temperature ; *Microbiota ; Ecotype ; }, abstract = {Mesoscale eddies, horizontally rotating currents sometimes referred to as "ocean weather," influence open ocean macronutrient distributions, primary production, and microbial community structure. Such eddies impact ecosystems like the North Pacific Subtropical Gyre, where year-round thermal stratification limits the mixing of subsurface macronutrients with surface waters. Populations of the dominant primary producer Prochlorococcus in the North Pacific Subtropical Gyre consist of genetic variants with differential adaptive traits to light intensity, temperature, and macronutrient availability. How Prochlorococcus population variants respond to transient, localized environmental changes, however, remains an open question. Leveraging microbial community phylogenetic, metagenomic, and metatranscriptomic data, we report here a consistent, specific enrichment of Prochlorococcus high-light I ecotypes around the deep chlorophyll maximum (DCM) in cyclonic eddies, but not adjacent anticyclonic eddies. The shallower DCM depths of cyclones had lower temperatures, higher light intensities, and elevated nutrient concentrations compared to adjacent anticyclones, which favored Prochlorococcus high-light I ecotype proliferation. Prochlorococcus high-light I ecotypes in the cyclone DCM exhibited unique genetic traits related to nitrogen metabolism and were enriched in gene transcripts associated with energy production, cell replication, and proliferation. Prochlorococcus gene transcripts involved in amino acid transport, metabolism, and biosynthesis were also elevated in the cyclone. These results suggest the potential importance of nitrogen metabolism in Prochlorococcus high-light I ecotype proliferation in cyclonic eddies. Our findings demonstrate how mesoscale eddies shape microbial community structure in the oligotrophic ocean and how Prochlorococcus communities respond to short-term localized environmental variability.}, } @article {pmid40414991, year = {2025}, author = {Rashid, MH and Pascottini, OB and Xie, L and Niazi, M and Lietaer, L and Comlekcioglu, U and Opsomer, G}, title = {Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18274}, pmid = {40414991}, issn = {2045-2322}, support = {2(3)/HRD/OSS-III/2022/HEC/83//Higher Education Commission, Pakistan/ ; KP 2020; FFB200048//Ghent University, Belgium/ ; BOF17/DOC/269//Ghent University, Belgium/ ; 12Y5220N//University of Antwerp, Belgium/ ; CSC; 202206300032//China Scholarship Council/ ; }, mesh = {Animals ; Cattle ; Female ; *Endometritis/microbiology/veterinary ; *Cattle Diseases/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Postpartum Period ; *Uterus/microbiology ; Bacteria/genetics/classification/isolation & purification ; *Microbial Interactions ; Metagenome ; }, abstract = {Clinical endometritis (CE) is associated with bacterial pathogens while the same has not been proved about subclinical endometritis (SCE). We aimed to use shotgun metagenomic sequencing to investigate the associations between potentially unidentified pathogens and SCE. Uterine cytobrush samples from multiparous Holstein cows (n = 23) were taken at 21 days in milk (DIM) and sequenced via the Illumina shotgun platform. At 36 DIM, the cows were diagnosed as CE (n = 7), SCE (n = 7), or healthy (n = 9). We did not find differences in the alpha and beta diversity of bacteria and eukaryotes among the health groups. Relative abundance of typical pathogens i.e. Fusobacterium, Peptoniphilus, Peptostreptococcus, and Trueperella was greater in CE than healthy controls. We did not find evidence of eukaryotic or viral association in infection, yet, distinct patterns of bacterial co-occurrence were observed among pathogenic and non-pathogenic bacteria. In CE cows, Wnt/catenin pathway had lower abundance than SCE or healthy cows. Our findings support that CE is characterized by domination of pathogenic bacteria that intercorrelate, whereas SCE is not associated with bacterial colonization.}, } @article {pmid40414843, year = {2025}, author = {Thompson, TP and Rice, CJ and Athanasakis, E and Mawhinney, J and Gilmore, BF and Fitzgerald, P and Skvortsov, T and Kelly, SA}, title = {The effect of sample type and location on industrial workplace sink and hand dryer microbiomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {325}, pmid = {40414843}, issn = {1471-2180}, mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Humans ; Workplace ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Hand Disinfection ; Hand/microbiology ; Metagenomics ; }, abstract = {One major issue in tackling antimicrobial resistance (AMR) is the ability to effectively track resistance spread in environments where surveillance is limited. Such environments include those experiencing high volumes of hand washing and drying from multiple users. This study characterised the microbial populations and antimicrobial resistomes of two different sample types from a pharmaceutical industrial site as part of an AMR environmental surveillance programme. Paired samples were collected from hand dryers and adjacent sinks in distinct sampling locations: from toilets adjacent to 'wet' labs, and locations associated with 'dry' activities. Microbial populations in hand dryers were significantly different to those of sinks, whereas there was no significant difference based on sample location. The opposite effect was observed for resistomes, where profiles differed significantly based on sample location, but not sample type. When both sample type and location were considered together, differences in microbiomes were driven primarily by hand dryer profiles from different locations. Analysis of metagenomically-assembled genomes revealed the presence of many poorly characterised organisms, and suggested no specific families predominated in terms of ARG carriage. This study emphasises the impact of human activities in determining the resistome of commonly used appliances, and the need for continued AMR surveillance programmes.}, } @article {pmid40413859, year = {2025}, author = {Merchant, M and Mande, SS and Sar, P}, title = {Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions.}, journal = {Chemosphere}, volume = {382}, number = {}, pages = {144429}, doi = {10.1016/j.chemosphere.2025.144429}, pmid = {40413859}, issn = {1879-1298}, mesh = {*Polyethylene/metabolism ; Waste Disposal Facilities ; Biodegradation, Environmental ; Anaerobiosis ; Biotransformation ; Aerobiosis ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; }, abstract = {Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.}, } @article {pmid40413728, year = {2025}, author = {Kousgaard, SJ and Dall, SM and Albertsen, M and Nielsen, HL and Thorlacius-Ussing, O}, title = {Fecal microbiota transplantation from a healthy pouch donor for chronic pouchitis: a proof-of-concept study.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2510464}, pmid = {40413728}, issn = {1949-0984}, mesh = {Humans ; *Pouchitis/therapy/microbiology ; *Fecal Microbiota Transplantation/adverse effects/methods ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Quality of Life ; Chronic Disease/therapy ; Gastrointestinal Microbiome ; Proof of Concept Study ; Treatment Outcome ; Tissue Donors ; Denmark ; }, abstract = {Chronic pouchitis is a common complication after ileal pouch-anal anastomosis (IPAA) with limited treatment options. In this case series, we aimed to investigate clinical and microbiome changes, as well as adverse events, associated with using fecal microbiota transplantation (FMT) from a donor with a normal functioning IPAA to induce remission in patients with chronic pouchitis. Methods The study was a case-series including a 4-week intervention period and 12-month follow-up. Patients with chronic pouchitis who met the inclusion criteria were recruited from the Department of Gastrointestinal Surgery at Aalborg University Hospital, Denmark. Participants received FMT derived from a donor with a normal functioning IPAA. Treatment was administered by enema daily for two weeks, then every other day for two more weeks. Disease severity and quality of life (QoL) were accessed at baseline and 30-day follow-up. Clinical remission was defined as Pouchitis Disease Activity Index (PDAI) <7. Fecal samples from participants, healthy donors, and the IPAA donor were analyzed using shotgun metagenomic sequencing. Results Three patients with chronic pouchitis were included and completed the treatment protocol and follow-up visits. At the 30-day follow-up, all participants achieved clinical remission with reduced endoscopic inflammation. The median total PDAI score decreased from 8 (range 10-8) at baseline to 6 (range 6-5) at 30 days. Two participants reported improved QoL, while one reported no change. Few mild, self-limited adverse events were reported by all participants during treatment, with no serious events. Principal component analysis of fecal samples distinguished two clusters: healthy donors and the IPAA donor, with participant samples forming a separate cluster Conclusion We observed that all participants achieved clinical remission with reduced endoscopic inflammation following a 4-week FMT intervention. Adverse events were mild and self-limited. Metagenomic analysis revealed distinct microbiome clusters between IPAA donor and recipients, both of which differed from those of healthy donors.}, } @article {pmid40413726, year = {2025}, author = {Zhang, DY and Li, D and Chen, SJ and Zhang, LJ and Zhu, XL and Chen, FD and Chen, C and Wang, Q and Du, Y and Xiong, JX and Huang, SM and Zhang, XD and Lv, YT and Zeng, F and Chen, RX and Huang, X and Mao, F and Zhou, S and Yao, Q and Huang, Y and Chen, R and Mo, Y and Xie, Y and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Bai, FH}, title = {Bacteroides uniformis-generated hexadecanedioic acid ameliorates metabolic-associated fatty liver disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2508433}, pmid = {40413726}, issn = {1949-0984}, mesh = {Humans ; Gastrointestinal Microbiome ; Animals ; *Bacteroides/metabolism/genetics ; Mice ; Male ; Female ; Middle Aged ; Feces/microbiology ; Liver/metabolism ; *Fatty Liver/microbiology/metabolism ; Fecal Microbiota Transplantation ; Prospective Studies ; Adult ; Metabolomics ; Mice, Inbred C57BL ; }, abstract = {Gut microbiota exerts a pivotal influence on the development of Metabolic Associated Fatty Liver Disease (MAFLD), although the specific contributions of individual bacterial strains and their metabolites remain poorly defined. We conducted stool shotgun metagenomic sequencing and plasma untargeted metabolomics in a large prospective cohort comprising 120 MAFLD patients and 120 matched healthy controls. The mechanisms and microbial-derived metabolites involved in MAFLD were further investigated through multi-omics analyses in vitro and in vivo. Distinct differences were identified in both the microbial community structure and metabolomic profiles between MAFLD patients and healthy controls. Bacteroides uniformis (B. uniformis) was the most significantly depleted species in MAFLD and negatively correlated with hepatic steatosis and BMI. MAFLD was characterized by marked disruptions in fatty acid and amino acid metabolism. Combined analysis of metabolomic and metagenomic data achieved high diagnostic accuracy for MAFLD and hepatic steatosis severity (AUC = 0.93). Transplantation of fecal microbiota from MAFLD subjects into ABX mice led to the onset of MAFLD-like symptoms, whereas B. uniformis administration alleviate disease progression by inhibiting intestinal fat absorption, FFA from eWAT influx into liver via the gut-liver axis, and IRE1α-XBP1s-mediated flipogenesis and ferroptosis, as confirmed by hepatic transcriptomic and proteomic analyses. Hexadecanedioic acid (HDA), potentially identified as a key metabolite produced by B. uniformis, ameliorated MAFLD symptoms. Mechanistically, B. uniformis-derived HDA also inhibited fat absorption and transported, and entered the liver via the portal vein to suppress IRE1α-XBP1s-mediated flipogenesis and ferroptosis. B. uniformis and its potential putative metabolite HDA may contribute to MAFLD progression modulation, through regulation of the IRE1α-XBP1s axis. This study provides new insights into the gut-liver axis in MAFLD and offers promising therapeutic targets based on specific microbes and their metabolites.}, } @article {pmid40413611, year = {2025}, author = {Ju, J and He, J and Ye, B and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Liu, L and Li, Y and Xia, M and Liu, Y}, title = {Microbial metabolism mediates the deteriorative effects of sedentary behaviour on insulin resistance.}, journal = {Clinical and translational medicine}, volume = {15}, number = {5}, pages = {e70348}, pmid = {40413611}, issn = {2001-1326}, support = {2023YFC3606300//National Key Research and Development Program of China/ ; 82330105//Key Project of National Natural Science Foundation of China/ ; Overseas//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 21HAA01094//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 2024A04J6477//Guangzhou Science and Technology Project/ ; }, mesh = {*Insulin Resistance/physiology ; Humans ; *Sedentary Behavior ; Male ; *Gastrointestinal Microbiome/physiology ; Adult ; }, abstract = {BACKGROUND: Prolonged sedentary time is a strong risk factor for insulin resistance. Recent evidence indicates that gut microbiota may influence the regulation of insulin sensitivity and demonstrates a distinct profile between sedentary and physically active individuals. However, whether and how microbial metabolism mediates the progression of insulin resistance induced by prolonged sedentary time remains unclear.

METHODS: 560 male participants without hypoglycaemic therapy were included, and insulin resistance was evaluated using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). The gut microbiota was identified through metagenomics, host genetic data were obtained using a genotyping array, and plasma metabolites were quantified by liquid chromatography mass spectrometry.

RESULTS: A panel of 15 sedentary-related species and 38 sedentary-associated metabolic capacities accounted for 31.68% and 21.48% of the sedentary time-related variation in HOMA-IR, respectively. Specifically, decreased Roseburia sp. CAG:471, Intestinibacter bartlettii, and Firmicutes bacterium CAG:83, but increased Bacteroides xylanisolvens related to longer sedentary time, were causally linked to the development of insulin resistance. Furthermore, integrative analysis with metabolomics identified reduced L-citrulline and L-serine, resulting from a suppression of arginine biosynthesis as key microbial effectors linking longer sedentary time to enhanced insulin resistance.

CONCLUSIONS: In summary, our findings provide insights into the mediating role of gut microbiota on the progression of insulin resistance induced by excessive sedentary time, and highlight the possibility of counteracting the detrimental effect of prolonged sedentary time on insulin resistance by microbiota-modifying interventions.

KEY POINTS: Prolonged sedentary time leads to a depletion of Roseburia sp. CAG:471 and Firmicutes bacterium CAG:83, and suppresses arginine biosynthesis. Decreased L-citrulline and L-serine function as key microbial effectors mediating the adverse effect of sedentary time on insulin sensitivity. Targeting gut microbiota holds promise to combat insulin resistance induced by excessive sedentary time.}, } @article {pmid40413198, year = {2025}, author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL}, title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {858}, pmid = {40413198}, issn = {2052-4463}, support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; }, abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.}, } @article {pmid40412963, year = {2025}, author = {Wang, C and Tian, Z and Luan, X and Zhang, H and Zhang, Y and Yang, M}, title = {Distribution of antibiotic resistance genes on chromosomes, plasmids and phages in aerobic biofilm microbiota under antibiotic pressure.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {647-659}, doi = {10.1016/j.jes.2024.10.008}, pmid = {40412963}, issn = {1001-0742}, mesh = {*Biofilms/drug effects ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes (ARGs) for blocking their environmental dissemination. The distribution of ARGs in chromosomes, plasmids, and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline, streptomycin, and tigecycline were revealed based on metagenomics analysis. Results showed that the plasmids harbored 49.2 %-83.9 % of resistomes, which was higher (p < 0.001) than chromosomes (2.0 %-35.6 %), and no ARGs were detected in phage contigs under the strict alignment standard of over 80 % identity used in this study. Plasmids and chromosomes tended to encode different types of ARGs, whose abundances all increased with the hike of antibiotic concentrations, and the variety of ARGs encoded by plasmids (14 types and 64 subtypes) was higher than that (11 types and 27 subtypes) of chromosomes. The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids, mediated by transposable and integrable transfer elements, which increased the co-occurrence of associated and unassociated ARGs. The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection, which should be a key target for blocking ARG dissemination.}, } @article {pmid40412639, year = {2025}, author = {Iriarte, J and Lundin, D and Martinez-Varela, A and Gónzalez, JM and Sánchez, P and Dachs, J and Vila-Costa, M}, title = {Entanglement of hydrocarbon-degrading bacteria and polycyclic aromatic hydrocarbons in the ocean.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {379}, number = {}, pages = {126512}, doi = {10.1016/j.envpol.2025.126512}, pmid = {40412639}, issn = {1873-6424}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Bacteria/metabolism/genetics/classification ; *Water Pollutants, Chemical/metabolism/analysis ; Biodegradation, Environmental ; Phylogeny ; Oceans and Seas ; Microbiota ; Metagenome ; }, abstract = {Knowledge of Earth's microbiomes' capacity to degrade aromatic compounds is limited by the lack of accurate tools for identifying degrading genes and their associated taxa. Additionally, these estimates are hardly compared to in situ background concentrations of polycyclic aromatic hydrocarbons (PAHs), particularly in oceanic waters. This knowledge is important for assessing the persistence of the widespread and abundant PAHs in the environment and their interactions with microbes. Here, we present a new tool to identify aromatic ring-hydroxylating dioxygenase α-subunit (arhdA) gene sequences by combining profile-based search with phylogenetic placement in a reference phylogeny. We identified arhdA-harboring taxa in both the Genome Taxonomy Database and the Malaspina Vertical Profiles Gene Database, a gene catalog derived from metagenomes collected during the Malaspina expedition. We found that multiple ubiquitous taxa in tropical and temperate oceans harbor arhdA. The comparison of arhdA gene abundances in seawater metagenomes with the field PAH concentrations showed that higher abundances of arhdA gene copies per cell were negatively correlated with 2-4 ring PAHs, consistent with the known degradation of lighter PAHs. Gene abundances were significantly higher in the particle-associated fraction than in the free-living fraction, suggesting particulate matter as a relevant reservoir of PAH degraders. Finally, we show that PAHs, together with other environmental variables, modulate the structure of oceanic microbial communities.}, } @article {pmid40410832, year = {2025}, author = {Chu, B and Ge, S and He, W and Sun, X and Ma, J and Yang, X and Lv, C and Xu, P and Zhao, X and Wu, K}, title = {Gut symbiotic bacteria enhance reproduction in Spodoptera frugiperda (J.E. Smith) by regulating juvenile hormone III and 20-hydroxyecdysone pathways.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {132}, pmid = {40410832}, issn = {2049-2618}, support = {2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; }, mesh = {Animals ; *Spodoptera/microbiology/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Ecdysterone/metabolism ; *Symbiosis ; Female ; Reproduction ; Enterobacter/isolation & purification/physiology ; Larva/microbiology ; Enterococcus/isolation & purification/physiology/genetics ; Klebsiella/isolation & purification/genetics/physiology ; Bacteria/classification/genetics ; *Juvenile Hormones/metabolism ; }, abstract = {BACKGROUND: The insect gut microbiota forms a complex, multifunctional system that significantly affects phenotypic traits linked to environmental adaptation. Strong reproductive potential underpins the migratory success, population growth and destructive impact of the fall armyworm, Spodoptera frugiperda (J.E. Smith). However, the precise role of gut bacteria in S. frugiperda reproductive processes, distribution and transmission dynamics remains unclear.

RESULTS: We examined the gut microbiota of S. frugiperda a major invasive agricultural pest, identifying Enterococcus, Enterobacter, and Klebsiella as core microorganisms present throughout its life cycle. These microbes showed heightened activity during the egg stage, early larval stages and pre-oviposition period in females. Using an axenic insect re-infection system, Enterococcus quebecensis FAW181, Klebsiella michiganensis FAW071 and Enterobacter hormaechei FAW049 were found to significantly enhance host fecundity, increasing egg production by 62.73%, 59.95%, and 56.71%, respectively. Metagenomic and haemolymph metabolomic analyses revealed a positive correlation between gut symbiotic bacteria and hormone metabolism in female S. frugiperda. Further analysis of metabolites in the insect hormone biosynthesis pathway, along with exogenous injection of juvenile hormone III and 20-hydroxyecdysone, revealed that gut microbes regulate these hormones, maintaining levels equivalent to those in control insects. This regulation supports improved fecundity in S. frugiperda, aiding rapid colonization and population expansion.

CONCLUSIONS: These findings emphasize the pivotal role of gut bacteria E. quebecensis FAW181, E. hormaechei FAW049, and K. michiganensis FAW071 in enhancing S. frugiperda reproduction by modulating JH III levels through JHAMT regulation and concurrently modulating the levels of 20E and its precursors via PHM. Our results provide novel insights into microbe-host symbiosis and pest management strategies for alien invasive species. Video Abstract.}, } @article {pmid40410138, year = {2025}, author = {Chen, AS and Kim, H and Nzabarushimana, E and Shen, J and Williams, K and Gurung, J and McGoldrick, J and Burke, KE and Yarze, JC and Nguyen, LH and Staller, K and Chung, DC and Xavier, RJ and Khalili, H}, title = {Association of distinct microbial and metabolic signatures with microscopic colitis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4644}, pmid = {40410138}, issn = {2041-1723}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AG068390/AG/NIA NIH HHS/United States ; P30DK043351//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01AG068390//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Metabolome ; Feces/microbiology ; *Colitis, Microscopic/microbiology/metabolism ; Aged ; Adult ; Case-Control Studies ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diarrhea/microbiology/metabolism ; Metabolomics ; Metagenomics ; Biomarkers/metabolism ; }, abstract = {Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.}, } @article {pmid40410126, year = {2025}, author = {Su, C and Zhou, H and Wang, Y and Duan, X and Jiang, T and Zhang, C and Gao, H and Kong, L and Wang, M and Guo, C}, title = {Contrasting Effects of Atmospheric Particulate Matter Deposition on Free-Living and Particle-Associated Bacteria in the South China Sea.}, journal = {Environmental science & technology}, volume = {59}, number = {22}, pages = {11016-11028}, doi = {10.1021/acs.est.4c12533}, pmid = {40410126}, issn = {1520-5851}, mesh = {*Particulate Matter ; *Bacteria ; China ; Atmosphere ; Seawater/microbiology ; }, abstract = {Atmospheric particulate matter (PM) deposition has become an important nutrient source in marine ecosystems, increasing particulate organic carbon and resource heterogeneity. However, their effects on marine bacterial communities remain unclear. In this study, by conducting on-board microcosm experiments with anthropogenic East Asian PM in the oligotrophic South China Sea, the response of particle-associated (PA) bacteria was investigated and compared with its free-living (FL) counterparts. Results showed that PM input increased nutrient heterogeneity, shifting bacterial community composition and lifestyle. Copiotrophic PA bacteria became more abundant and contributed a disproportionately higher percentage to total bacterial production despite a decline in total bacterial abundance. FL bacteria showed increased diversity, shifting from oligotrophs to copiotrophs, while PA bacteria displayed reduced diversity and nondirectional compositional changes, suggesting their distinct assembly mechanisms in response to external nutrient inputs. Metagenomic analysis further revealed that PM drives a shift toward a copiotrophic, particle-attached lifestyle with upregulated pathways for chemotaxis, motility, and biofilm formation. Notably, PM addition also increased the relative abundance of oil-degrading taxa. These findings reveal the complexity of microbial responses to environmental perturbations and underscore the need to consider unique ecological niches and bacterial lifestyles.}, } @article {pmid40409349, year = {2025}, author = {Zhou, S and Wang, K and Huang, J and Xu, Z and Yuan, Q and Liu, L and Wang, Z and Miao, J and Wang, H and Wang, T and Guan, W and Ding, C}, title = {Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2508949}, pmid = {40409349}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/metabolism/drug therapy/pathology/microbiology ; Humans ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Indoles/metabolism/pharmacology/administration & dosage ; STAT3 Transcription Factor/metabolism ; Cell Proliferation/drug effects ; Tryptophan/metabolism ; Cell Line, Tumor ; Male ; Female ; Receptors, Aryl Hydrocarbon/metabolism ; Cell Movement/drug effects ; Apoptosis/drug effects ; Metabolic Reprogramming ; }, abstract = {Research indicates that abnormal gut microbiota metabolism is linked to colorectal cancer (CRC) progression, but the role of microbiota-related tryptophan metabolism disruption remains unclear. Using metagenomic sequencing and targeted Trp metabolomics, our research identified that CRC patients had abnormal indole-3-lactic acid (ILA) levels, which were related to tumor malignancy. Exogenous ILA administration suppressed CRC development in AOM/DSS induced and xenograft mice models. Furthermore, in vitro experiments demonstrated that ILA inhibits tumor cell proliferation, migration, and anti-apoptotic capabilities. Mechanistically, ILA appears to directly occupy the phosphorylation sites of STAT3, leading to a reduction in intracellular phosphorylated STAT3 (p-STAT3) levels and the inhibition of the HK2 pathway, thereby downregulating glucose metabolism in cancer cells. Notably, this inhibition is independent of the aryl hydrocarbon receptor (AHR). In conclusion, our research findings demonstrate that alterations in tryptophan metabolism among CRC patients can influence tumor progression and reveal a novel mechanism through which ILA exerts its inhibitory effects on CRC. These findings offer new insights into the role of gut microbiota in CRC and identify potential clinical therapeutic targets.}, } @article {pmid40409085, year = {2025}, author = {Xie, Y and Wang, T and Guo, C and Chu, C and Liu, Z and Jiang, L and Deng, Y and Yi, J}, title = {Metagenomic insights into the microorganisms responsible for producing amino acid nitrogen during sufu fermentation.}, journal = {Food chemistry}, volume = {487}, number = {}, pages = {144763}, doi = {10.1016/j.foodchem.2025.144763}, pmid = {40409085}, issn = {1873-7072}, mesh = {Fermentation ; *Amino Acids/metabolism ; *Nitrogen/metabolism/analysis ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; *Fungi/metabolism/genetics/classification/isolation & purification ; Microbiota ; }, abstract = {Amino acid nitrogen (AAN), a key contributor to umami taste, plays a central role in flavor development during sufu fermentation. Given the critical influence of microbial metabolism on flavor formation, this study employed metagenomic analysis to investigate the mechanisms of AAN generation. During sufu fermentation, the AAN content increased significantly, reaching a final concentration of 0.56 g/100 g. Metagenomic analysis revealed that both bacterial (e.g., Dysgonomonas macrotermitis, Lactococcus lactis) and fungal (e.g., Rhizopus arrhizus) species were the core microbiota driving AAN formation. These microorganisms encoded abundant proteases and amino acid hydrolases essential for AAN metabolism. Functional profiling highlighted carbohydrate and amino acid metabolism as the dominant pathways in flavor formation. Notably, glutamate synthesis was associated with pathways ko00220 and ko00250, mediated by glutamate synthetase (EC 1.4.1.13) and glutamine synthetase (EC 6.3.1.2). These findings elucidate the microbial enzymatic mechanisms-particularly amino acid transformations-underlying sufu's umami taste development during fermentation.}, } @article {pmid40407311, year = {2025}, author = {Li, H and Wang, Z and He, S and Zhao, X and Wu, Q and Sun, Y and Fan, Y and Hu, X and Tian, Z and Zhang, S}, title = {Unraveling gut microbiome alterations and metabolic signatures in hereditary transthyretin amyloidosis.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0230224}, pmid = {40407311}, issn = {2165-0497}, support = {20220484031//Beijing Nova Program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Male ; Female ; Middle Aged ; *Amyloid Neuropathies, Familial/microbiology/metabolism ; Aged ; *Metabolome ; Taurine/blood/metabolism ; gamma-Aminobutyric Acid/blood ; Bacteria/classification/genetics/metabolism/isolation & purification ; Glutamic Acid/metabolism ; Adult ; Metagenomics ; }, abstract = {UNLABELLED: Hereditary transthyretin amyloidosis (hATTR) is a rare, often fatal disease characterized by the abnormal aggregation of atypical transthyretin fibrils. Given the variability in the penetrance and clinical manifestations of hATTR, the role of nongenetic factors, particularly those related to the gut microbiota, warrants investigation. We conducted a cross-sectional study, examining the untargeted serum metabolome and gut metagenome in 13 patients with hATTR and 22 healthy controls. Significant disparities were observed in both the serum metabolome and gut microbiome of individuals with hATTR when compared to healthy controls. Notably, the serum levels of gamma-aminobutyric acid (GABA) and taurine were markedly decreased in the hATTR group, with the most pronounced reduction in those exhibiting hATTR-related cardiac amyloidosis. Additionally, commensals such as Bifidobacterium pseudocatenulatum, Lactobacillus rogosae, and Hungatella hathewayi were significantly diminished in hATTR patients and were positively correlated with the metabolite module containing GABA and taurine. Metagenomic and metabolomic pathway enrichment analyses collectively revealed disruptions in glutamate and taurine metabolism in hATTR. Our findings imply that patients with hATTR may exhibit metabolic irregularities in glutamate and taurine, potentially associated with an imbalance in the gut microbiota.

IMPORTANCE: Hereditary transthyretin amyloidosis (hATTR) is influenced not only by genetic factors but also by environmental or host factors during its onset and progression. Previous studies have independently examined the metabolome or gut microbiome in hATTR, but the interplay between the microbiota and metabolism under this condition remains largely unknown. Our cross-sectional study represents the first comprehensive integration of gut metagenome and serum metabolome analyses in hATTR patients. We observed disturbances in glutamate and taurine metabolism among these patients, which correlated with distinctive shifts in the gut microbiota. This study offers insights into the intricate dynamics among gut dysbiosis, metabolic imbalances, and the progression of hATTR, suggesting directions for future research into the underlying mechanisms and therapeutic strategies.}, } @article {pmid40407096, year = {2025}, author = {Creskey, M and Silva Angulo, F and Wu, Q and Tamming, L and Fekete, EEF and Cheng, K and Ning, Z and Wang, A and Brito Rodrigues, P and de Rezende Rodovalho, V and Ramirez Vinolo, MA and Figeys, D and Li, X and Trottein, F and Zhang, X}, title = {Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2505117}, pmid = {40407096}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology ; Cricetinae ; *Proteomics/methods ; SARS-CoV-2 ; Feces/microbiology ; Age Factors ; Metagenomics ; Disease Models, Animal ; Mesocricetus ; Male ; }, abstract = {The gut microbiome's pivotal role in health and disease is well established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32,419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the interactions between the microbiome and host in SARS-CoV-2 infection. Altogether, this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.}, } @article {pmid40406519, year = {2025}, author = {Song, T and Yin, L and Zhou, X and Tao, X and Tie, D and Zhang, J and Jiang, L}, title = {Microbiota profiling from biopsied tissues in complex infections: a diagnostic and prognostic analysis through metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1567981}, pmid = {40406519}, issn = {2235-2988}, mesh = {Humans ; Male ; Retrospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; Prognosis ; *High-Throughput Nucleotide Sequencing/methods ; Biopsy ; Adult ; Aged ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Coinfection/microbiology/diagnosis ; Fungi/isolation & purification/genetics/classification ; Viruses/isolation & purification/genetics/classification ; Aged, 80 and over ; Sensitivity and Specificity ; *Communicable Diseases/diagnosis/microbiology ; }, abstract = {BACKGROUND: Infectious diseases that require tissue biopsy are usually more difficult to diagnose through conventional microbiological tests (CMT), and knowledge of the infection microbiota pattern from biopsied tissues remains incomplete. Our study aimed to investigate the diagnostic and prognostic value of metagenomic next-generation sequencing (mNGS), characterize the microbiota profile from biopsied tissues, and examine its relationship with clinical outcomes.

METHODS: This retrospective cohort study included 110 patients who underwent tissue biopsy and sent both mNGS and CMT due to suspected complex infection. Microbiota patterns were illustrated via unsupervised hierarchical clustering analysis. Multivariate regression analysis was used to investigate the effect measures.

RESULTS: The sensitivity of mNGS was significantly higher than that of CMT regarding bacteria (87.23% vs 40.43%, P=0.01), viruses (100% vs 5.56%, P<0.001), and fungi (87.5% vs 28.6%, P=0.04). Polymicrobial infection accounted for 45.2% (33/73) of the infection samples. In skeletal articular biopsied tissues, Staphylococcus presented the highest mean abundance among different species of bacteria (21.2% of all bacterial reads, standard deviation (SD) 38.9). Anaerobic bacteria (24.0%, SD 25.9) represented the most common bacteria in biopsied tissue from the lung or mediastinum. The presence of gram-negative bacteria (adjusted OR 5.21, 95% CI 1.39-19.43, P=0.01), Enterobacteriaceae (adjusted OR 5.71, 95% CI 1.17-28.03, P=0.03) and Staphylococcus (adjusted OR 8.64, 95% CI 1.95-38.34, P=0.005) was associated with an increased risk of treatment failure. Early mNGS sampling within 7 days after admission was associated with a significantly decreased risk of all-cause mortality (HR 0.18, 95% CI 0.04-0.94; P=0.04), treatment failure (OR 0.17, 95% CI 0.05-0.66; P=0.01), and increased probability of clinical resolution (OR 3.03, 95% CI 1.24-7.40; P=0.01).

CONCLUSION: mNGS demonstrates significant diagnostic and prognostic efficacy in patients undergoing tissue biopsy for suspected complex infections. The presence of Gram-negative bacteria, Enterobacteriaceae, and Staphylococcus is associated with a higher probability of treatment failure, which underscores the advantage of using mNGS to guide more aggressive antibiotic strategies.}, } @article {pmid40405096, year = {2025}, author = {Yasmin, A and Rahman, MS and Kador, SM and Ahmed, MM and Moon, MEK and Akhter, H and Sultana, M and Begum, A}, title = {Metagenomic insights into microbial diversity and potential pathogenic transmission in poultry farm environments of Bangladesh.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {318}, pmid = {40405096}, issn = {1471-2180}, mesh = {Bangladesh ; Animals ; *Bacteria/genetics/classification/isolation & purification/drug effects/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Farms ; *Poultry/microbiology ; *Microbiota/genetics ; *Metagenomics ; *Poultry Diseases/transmission/microbiology ; Biodiversity ; Soil Microbiology ; DNA, Bacterial/genetics ; }, abstract = {The microbiome plays a critical role in poultry health and productivity, influencing growth, immunity, and the overall farm ecosystem. This study investigated microbial diversity, antibiotic resistance pathways, and functional potential across various components of poultry ecosystems-cloacal swabs, droppings, feed, hand swabs, soil, and water-in different districts of Bangladesh. Using 16S rRNA gene amplicon sequencing, we identified 2,745 Operational Taxonomic Units (OTUs) and analyzed microbial richness, community structure, and functional pathways. Alpha diversity metrics revealed that droppings exhibited the highest microbial richness (726 OTUs in Noakhali), while feed samples showed the lowest diversity (211 OTUs). Beta diversity analysis indicated significant differences in microbial composition across sample sources, with PERMANOVA confirming that sample origin accounted for 51.45% of the variability (p < 0.001). Proteobacteria dominated the microbial communities (48.36%), followed by Firmicutes (19.83%) and Cyanobacteria (12.02%). Key genera of concern, such as Enterobacter (26.62% in hand swabs), Acinetobacter (30.87% in cloacal swabs), and Shigella (22.89% in cloacal swabs), were identified, highlighting potential contamination and zoonotic risks. Conversely, beneficial genera like Lactobacillus (36.89% in feed) and Enterococcus (10.78% in droppings) were prevalent, suggesting roles in gut health and nutrient cycling. Functional pathway analysis (KEGG) revealed that carbohydrate and amino acid metabolism were highly active in droppings and feed, reflecting nutrient utilization. Antimicrobial resistance (AMR) pathways, such as 23S rRNA-methyltransferase and multidrug efflux pumps, were widespread, with pathogenic genera (Enterobacter, Acinetobacter, Shigella, Pseudomonas) showing strong positive correlations with AMR pathways. These findings underscore the influence of environmental factors on microbial diversity and functional potential in poultry farming. The study highlights the need for improved management practices and biosecurity measures to mitigate risks associated with microbial pathogens and antimicrobial resistance, ultimately supporting healthier and more sustainable poultry production in Bangladesh.}, } @article {pmid40405076, year = {2025}, author = {Li, J and Chen, Z and Yan, X and Chen, Q and Chen, C and Liu, H and Shen, J}, title = {Effects of USP25 knockout on the gut microbial diversity and composition in mice.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {315}, pmid = {40405076}, issn = {1471-2180}, support = {2022J011443//Natural Science Foundation of Fujian Province/ ; 2024J011450//Natural Science Foundation of Fujian Province/ ; 2024112//Medical Research Foundation of Putian University/ ; 2024104//Medical Research Foundation of Putian University/ ; 82301785//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Mice, Inbred C57BL ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Ubiquitin Thiolesterase/genetics/deficiency ; Biodiversity ; Male ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in host health. Recent study revealed that ubiquitin-specific protease 25 (USP25) deficiency affected colonic immune responses and resistance to certain bacterial infection. This study aimed to investigate the impact of USP25 gene deletion on the gut microbiota of mice, utilizing 16 S rRNA amplicon sequencing and metagenomic sequencing to provide a comprehensive analysis of microbial diversity, composition and functional characteristics.

METHODS: We collected fecal samples from 10 wild type (WT) C57BL/6J mice and 10 USP25[-/-] mice (C57BL/6J-Usp25[em1]cyagen) for 16 S rRNA amplicon sequencing. Subsequently, the 6 of the 20 samples underwent further analysis using metagenomic sequencing.

RESULTS: Our results revealed significant differences in the gut microbiota between USP25 knockout (KO) mice and wild-type (WT) controls, with KO mice exhibiting 1,858 unique amplicon sequence variants (ASVs) compared to 1,723 in WT mice. Notably, the KO group displayed a higher tendency for biofilm formation and a greater proportion of gram-negative bacteria, while the WT group demonstrated enhanced stress tolerance and a higher presence of gram-positive bacteria. Functional prediction analyses indicated an increase in antibiotic resistance genes in the KO mice, particularly for tetracycline, cephalosporin, and sulfonamides, suggesting a potential risk for clinical antibiotic treatment efficacy. Moreover, KEGG pathway enrichment analysis revealed significant enrichment for fructose and mannose metabolism, streptomycin biosynthesis in the KO group. Furthermore, an increase in protective microbes alongside a decrease in potential pathogens in the KO microbiota hinted at altered immune responses due to USP25 deletion.

CONCLUSION: Our findings elucidate the essential role of USP25 in modulating gut microbiota composition and function, providing insights for future therapeutic strategies targeting gut microbiota in disease contexts.

CLINICAL TRAIL NUMBER: Not applicable.}, } @article {pmid40404683, year = {2025}, author = {Terbtothakun, P and Visedthorn, S and Klomkliew, P and Chanchaem, P and Sawaswong, V and Sivapornnukul, P and Sunantawanit, S and Khamwut, A and Rotcheewaphan, S and Kaewsapsak, P and Payungporn, S}, title = {Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17772}, pmid = {40404683}, issn = {2045-2322}, support = {HEA_FF_68_100_3000_016//Thailand Science research and Innovation Fund, Chulalongkorn University/ ; B05-F640122//The National Science, Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources and Institutional Development, Research and Innovation/ ; GA68/047//The Ratchadapisek Sompotch Fund, Faculty of Medicine, Chulalongkorn University/ ; }, mesh = {Humans ; *Sputum/microbiology ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis/microbiology/diagnosis ; *Fungi/genetics/isolation & purification/classification ; *Bacteria/genetics/classification/isolation & purification ; Male ; Female ; Mycobacterium tuberculosis/genetics/isolation & purification ; Middle Aged ; Adult ; }, abstract = {Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs, and inability to detect co-infections. This study utilizes full-length 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing based on Oxford Nanopore Technologies (ONT) to analyze clinical metagenomics of sputum microbiota from patients suspected with TB Infection. Our findings highlight the potential of ONT for profiling microbial communities associated with TB infection. The MTB group exhibited a significant abundance of Mycobacterium tuberculosis (M. tuberculosis) and Stenotrophomonas maltophilia. In contrast, Prevotella melaninogenica, Veillonella parvula, Corynebacterium striatum and Pseudomonas aeruginosa were more abundant in the negative samples. Fungal analysis revealed Candida orthopsilosis was enriched in MTB samples, while Aureobasidium leucospermi and Wallemia muriae predominated in negative samples. Correlation network analysis revealed M. tuberculosis exhibits positive and negative correlations with other microbial species, suggesting cooperative and competitive interactions that may influence microbial community dynamics and disease progression in TB patients. This study demonstrates the promise of ONT-based clinical metagenomics for rapid, comprehensive detection of bacterial and fungal co-infections, addressing limitations of conventional diagnostics and improving outcomes.}, } @article {pmid40404632, year = {2025}, author = {Dillard, LR and Glass, EM and Kolling, GL and Thomas-White, K and Wever, F and Markowitz, R and Lyttle, D and Papin, JA}, title = {Genome-scale metabolic network reconstruction analysis identifies bacterial vaginosis-associated metabolic interactions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4768}, pmid = {40404632}, issn = {2041-1723}, support = {R01-AI154242//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01-AT010253//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; NRT-ROL 2021791//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1 T 32 GM 145443-1//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 5T32GM136615-03//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1842490//National Science Foundation (NSF)/ ; }, mesh = {*Vaginosis, Bacterial/microbiology/metabolism ; Humans ; Female ; *Metabolic Networks and Pathways/genetics ; Vagina/microbiology ; Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metabolomics ; Metagenomics ; Genome, Bacterial ; Computer Simulation ; }, abstract = {Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women's health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of BV-associated bacterial metabolic interactions via genome-scale metabolic network reconstructions (GENREs). While most efforts to characterize symptomatic BV (and thus guide therapeutic intervention by identifying responders and non-responders to treatment) are based on genomic profiling, our in silico simulations reveal functional metabolic relatedness between species as quite distinct from genetic relatedness. We grow several of the most common co-occurring bacteria (Prevotella amnii, Prevotella buccalis, Hoylesella timonensis, Lactobacillus iners, Fannyhessea vaginae, and Aerrococcus christenssii) on the spent media of Gardnerella species and perform metabolomics to identify potential mechanisms of metabolic interaction. Through these analyses, we identify BV-associated bacteria that produce caffeate, a compound implicated in estrogen receptor binding, when grown in the spent media of other BV-associated bacteria. These findings underscore the complex and diverse nature of BV-associated bacterial community structures and several of these mechanisms are of potential significance in understanding host-microbiome relationships.}, } @article {pmid40403370, year = {2025}, author = {Liang, X and Li, B and Dong, X and Zhao, X and Li, H and Ye, Y and Ma, H and Ran, S and Li, J}, title = {Impact of microplastics exposure on the reconfiguration of viral community structure and disruption of ecological functions in the digestive gland of Mytilus coruscus.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138692}, doi = {10.1016/j.jhazmat.2025.138692}, pmid = {40403370}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Mytilus/virology/drug effects ; Animals ; Biofilms/drug effects ; *Water Pollutants, Chemical/toxicity ; Digestive System/virology/drug effects ; *Virome/drug effects ; *Viruses/genetics/drug effects ; }, abstract = {Microplastics (MPs) pose ecological risks by serving as viral vectors and disrupting host microbiomes. This study investigated the impact of MPs on the digestive gland virome of Mytilus coruscus through an in situ exposure experiment on Xixuan Island, Zhoushan, China, using polyethylene MPs and metagenomic sequencing. MPs biofilms were dominated by lytic viruses (> 99 %) with low diversity (Shannon index = 4.10 ± 0.39), whereas digestive glands harbored a more diverse virome (Shannon index = 7.26 ± 1.26). MPs ingestion significantly reduced virome diversity and altered viral community composition. Functional analysis showed that MPs biofilms were enriched in genes related to genetic processing, carbohydrate metabolism and membrane biogenesis, while transcription- and replication-related genes declined (P < 0.05) in digestive glands post-ingestion. MPs biofilms carried abundant antibiotic resistance genes (ARGs) and virulence factors, selectively enriching multidrug resistance genes (efrA, patB) while reducing functional viral gene abundance. Metal (Zn, Hg, As) and biocide resistance genes were prevalent in MPs biofilms but declined post-ingestion. Additionally, MPs ingestion weakened microbial network stability, potentially impairing immune regulation and metabolic homeostasis. These findings underscore MPs' role in shaping viral communities and spreading resistance genes, heightening ecological risks in marine environments.}, } @article {pmid40402042, year = {2025}, author = {Moosavi, D and Curtis, KR and Randolph, TW and Kahsai, OJ and Ammar, H and Lim, U and Cheng, I and Wilkens, LR and Le Marchand, L and Lampe, JW and Hullar, MAJ}, title = {Stability and Variability of the Human Fecal Microbiome over 2 Years in the Multiethnic Cohort Study: A Metagenomic Analysis.}, journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {34}, number = {8}, pages = {1386-1394}, pmid = {40402042}, issn = {1538-7755}, support = {P01 CA168530/CA/NCI NIH HHS/United States ; P30 CA015704/CA/NCI NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; P01 CA168530/CA/NCI NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; 3U01 CA164973-09S2//National Cancer Institute (NCI)/ ; T32 CA0924080//National Cancer Institute (NCI)/ ; //Fred Hutchinson Cancer Center (FHCRC)/ ; P30 CA015704/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Feces/microbiology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Aged ; *Metagenomics/methods ; Middle Aged ; Cohort Studies ; }, abstract = {BACKGROUND: Understanding the longitudinal variability of the gut microbiome is essential for advancing microbiome-based measurements and designing robust sampling protocols in observational and intervention studies of cancer and other health outcomes. The aim of this study was to explore the temporal variability and stability of the fecal microbiome over a 2-year period using intraclass correlation (ICC) analysis of metagenomic sequencing data.

METHODS: We studied 25 older adults from the Multiethnic Cohort Adiposity Phenotype Study (2013-2016). Stool samples were collected every 6 months over a 2-year period (five samples) and analyzed using metagenomic sequencing. The temporal stability was evaluated using ICCs across taxonomic levels, diversity, and functional genes and pathways.

RESULTS: The microbial community showed stability in α diversity and overall structure, with no significant changes observed across time points (Shannon diversity, P = 0.95). Taxonomic composition showed strong reliability over time, with median ICCs of 0.7 at the genus level and 0.75 at the species level. Functional genes also demonstrated good stability (median ICC = 0.68). However, microbial pathways were more variable with a fair median ICC of 0.49.

CONCLUSIONS: Although the fecal microbiome was generally stable, some taxa and functions were more dynamic and responsive to external influences.

IMPACT: Findings highlight the need for reliable microbiome measurements and sampling strategies to reduce bias in studies of the microbiome and cancer.}, } @article {pmid40401771, year = {2025}, author = {Callens, M and Le Berre, G and Van den Bulcke, L and Lolivier, M and Derycke, S}, title = {An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14126}, doi = {10.1111/1755-0998.14126}, pmid = {40401771}, issn = {1755-0998}, support = {RT/24/DNASense_ILVO//Belgian Federal Science Policy Office/ ; //Biodiversa+/ ; //Belgian Federal Public Service Economy/ ; BAR0159//Directorate-General for Regional Policy of the European Union/ ; }, abstract = {DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.}, } @article {pmid40399402, year = {2025}, author = {Jarmukhanov, Z and Vinogradova, E and Mukhanbetzhanov, N and Kozhakhmetov, S and Khassenbekova, D and Kushugulova, A}, title = {Parity influences postpartum adaptations in the maternal gut microbiota.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17636}, pmid = {40399402}, issn = {2045-2322}, support = {AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Female ; Humans ; *Gastrointestinal Microbiome ; *Postpartum Period/physiology ; Pregnancy ; Adult ; *Parity ; *Adaptation, Physiological ; Bacteria/genetics/classification ; Milk, Human ; }, abstract = {The gut microbiome undergoes substantial modifications during pregnancy, yet its postpartum adaptations remain poorly understood, particularly with respect to the influence of parity. Here, we investigated the impact of childbirth history on maternal gut microbiome composition and function one month postpartum. By conducting metagenomic sequencing analysis on 60 participants (34 postpartum mothers and 26 controls), we demonstrated significant differences in microbial diversity and community structure between postpartum mothers and control, as well as subtle differences between first-time mothers and multiple-birth mothers. We identified parity-specific signatures, with first-time mothers showing enrichment in Dysosmobacter welbionis, Candidatus Saccharibacteria, and Anaerotruncus species. Functional analysis revealed distinct metabolic reprogramming patterns, including increased amino acid biosynthesis and modified fermentation pathways supporting postpartum recovery. We observed significant correlations between specific bacterial taxa and metabolic pathways, particularly in energy metabolism and immune modulation. Notably, the enhanced capacity for short-chain fatty acid production in primiparous mothers, mediated by Anaerotruncus and Dysosmobacter welbionis, suggests a potential role in shaping breast milk composition, which may influence neonatal development. These findings establish the concept of parity-dependent microbiome programming and provide insights into the biological mechanisms underlying maternal adaptation to pregnancy and childbirth.}, } @article {pmid40398297, year = {2025}, author = {Shen, Y and Li, Y and Xiao, J and Li, J and Wu, Y and Wu, Y and Tang, H and Fang, X and Wang, L and Gong, Y and Chen, H and Yan, X}, title = {Comparative microbiomic analysis of fecal microbiota associated with abdominal fat in ducks.}, journal = {Poultry science}, volume = {104}, number = {8}, pages = {105282}, pmid = {40398297}, issn = {1525-3171}, mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; *Abdominal Fat/physiology ; Adiposity ; Meat ; Feces ; *Bacteria/classification/genetics/isolation & purification ; Female ; }, abstract = {The gut microbiota, which features complex community structures, colonizes the duck intestine and plays a crucial role in metabolism, immune regulation, and meat quality. Gut-microbiota-regulated abdominal fat deposition is a key factor that affects the meat quality of livestock and poultry. We used 16S rDNA and metagenomic sequencing to investigate the microbial community characteristics of 187 fecal samples from 10 Chinese indigenous duck breeds (five breeds for each of the high/low abdominal fat categories). We explored the relationship between fecal microbiota and abdominal fat deposition. The α diversity of the fecal microbiome in high abdominal fat ducks (HAF) was higher than that in low abdominal fat ducks (LAF). The fecal microbiota and function were also significantly different. At the phylum level, Actinobacteria was significantly enriched in HAF, whereas Proteobacteria, Candidatus, Saccharibacteria, and Fusobacteria were abundant in LAF. At the genus level, Lactobacillus, Alistipes, Corynebacterium, and Lachnoclostridium were more abundant in HAF than in LAF. The Streptococcus, Campylobacter, Helicobacter, Enterobacter, Gallibacterium, and Escherichia genera were significantly enriched in LAF. Microbial functional analysis indicated that the HAF fecal microbiota was mainly involved in carbohydrate, nucleotide, lipid, amino acid, terpenoids, polyketides, and xenobiotic metabolism. In addition, bacteria related to signal transduction, cofactor and vitamin metabolism, and infectious disease were enriched in LAF. This study revealed the relationship between gut microbiota and abdominal fat deposition in ducks. Our findings lay a foundation for the abdominal fat deposition mechanism in ducks and provide a reference for Chinese indigenous duck husbandry.}, } @article {pmid40397921, year = {2025}, author = {Abdillah, A and Ravaux, I and Mokhtari, S and Ranque, S}, title = {Do Malassezia yeasts colonize the guts of people living with HIV?.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0322982}, pmid = {40397921}, issn = {1932-6203}, mesh = {Humans ; *Malassezia/isolation & purification/genetics ; *HIV Infections/microbiology/complications/immunology ; Female ; Male ; Adult ; Feces/microbiology ; Middle Aged ; Immunocompromised Host ; Metagenomics ; *Gastrointestinal Microbiome ; Prospective Studies ; }, abstract = {Malassezia yeasts are commensals of human skin. In contrast to culture-based studies, metagenomic studies have detected abundant Malassezia reads in the gut, especially in patients living with HIV. Whether Malassezia colonizes and persists in the gut remains an open question. This study aimed to describe the influence of HIV-associated immunodeficiency on gut colonization by Malassezia and to assess whether Malassezia are alive. Stool samples were prospectively collected over one-five visits from ten controls and 23 patients living with HIV (10 had CD4 < 200/mm3 and 13 had CD4 > 500/mm3). Each sample was cultured and subjected to Malassezia viability PCR and both fungal and bacterial metabarcoding. Abundant M. furfur colonies were cultured from an HIV-immunocompromised patient. M. furfur and M. globosa were isolated in very low quantities from healthy volunteers. Viability Malassezia-specific qPCR was positive in three HIV-immunocompromised patients. Metagenomic analyses showed that Malassezia reads were significantly more abundant in immunocompromised patients living with HIV and erratic over time in all participants. Our findings emphasise that Malassezia are rarely cultured from human stool samples, despite the use of specific culture media. Although HIV-related immunosuppression appears to be associated with the presence of Malassezia, these yeasts do not persist and colonise the gut, even in immunocompromised patients.}, } @article {pmid40396743, year = {2025}, author = {Zhang, T and Han, Y and Peng, Y and Deng, Z and Shi, W and Xu, X and Wu, Y and Dong, X}, title = {The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0157124}, pmid = {40396743}, issn = {2379-5077}, support = {No. 3502Z202373076//Natural Science Foundation of Xiamen, China/ ; No. 2023J06042//Natural Science Foundation of Fujian Province/ ; No. 42376115, No. 92351304//National Natural Science Foundation of China/ ; No. 2022025, No. 2023022//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; No. 2021R51008//Zhejiang Provincal High-level Talent Special Support Plan/ ; }, mesh = {*Bacteria/pathogenicity/genetics/drug effects ; Virulence Factors/genetics ; *Seawater/microbiology ; Metagenome ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Interspersed Repetitive Sequences ; Geologic Sediments/microbiology ; Gene Transfer, Horizontal ; Microbiota ; }, abstract = {UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.

IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.}, } @article {pmid40396735, year = {2025}, author = {Zhang, J and Chen, B-Y and Zhi, M-F and Lin, W-Z and Li, Y-L and Ye, H-L and Xu, S and Zhu, H and Zhou, L-J and Du, L-J and Meng, X-Q and Liu, Y and Feng, Q and Duan, S-Z}, title = {Linking oral microbiota to periodontitis and hypertension unveils that Filifactor alocis aggravates hypertension via infiltration of interferon-γ[+] T cells.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0008425}, pmid = {40396735}, issn = {2379-5077}, support = {82330015,81991503,81991500//National Natural Science Foundation of China/ ; 2023YFA1801100,2023YFA1801104//National Key Research and Development Program of China/ ; BX20230226//China National Postdoctoral Program for Innovative Talents/ ; SHSMU-ZDCX20212500//Innovative Research Team of High-level Local University in Shanghai (Innovative Research Team of High-level Local Universities in Shanghai)/ ; }, mesh = {*Hypertension/microbiology/immunology/complications ; *Periodontitis/microbiology/complications/immunology ; Humans ; Animals ; *Interferon-gamma/metabolism ; *Microbiota ; Male ; Mice ; Female ; Middle Aged ; *Clostridiales ; *T-Lymphocytes/immunology/metabolism ; *Mouth/microbiology ; Saliva/microbiology ; Disease Models, Animal ; }, abstract = {UNLABELLED: Periodontal disease (PD), an inflammatory disease initiated by oral microbiota, may aggravate hypertension (HTN). Few studies were employed to characterize the oral microbiota in hypertensive patients with periodontitis. To investigate the interplay between oral microbiota and hypertension in individuals with periodontitis, we initiated a metagenomic sequencing study on subgingival plaque and saliva samples sourced from HTN patients and those with hypertension and periodontitis (PDHTN). Our primary objective was to characterize species serving as pivotal links (bridge species) in exacerbating hypertension induced by periodontal disease. Within subgingival plaque and saliva specimens, we pinpointed 31 and 28 bridge species, respectively. Furthermore, we noted a decrease in the abundance of nitrate-reducing bacteria, such as Actinomyces spp., Rothia spp., and Veillonella spp., in PDHTN samples. Employing network analysis, we distinguished distinct polymicrobial clusters within the two patient groups. These bridge species coalesced into polymicrobial clusters, revealing intricate symbiotic and competitive relationships. To substantiate our findings, we leveraged an angiotensin II-infused animal model of ligature-induced periodontitis (LIP), confirming the contributory role of Filifactor alocis-a selectively analyzed subgingival bridge species-in exacerbating hypertension and upregulating the frequency of renal CD4[+]IFNγ[+] and CD8[+]IFNγ[+] T cells. Our study screened a list of species linking PD and HTN. PD may aggravate HTN by decreasing the abundance of nitrate-reducing bacteria and increasing the abundance of pathogens. Using an animal model, we demonstrated that F. alocis aggravates HTN via the accumulation of IFNγ[+] T cells in the kidneys.

IMPORTANCE: Both periodontal disease and hypertension are widely prevalent all over the world. PD may aggravate the development of HTN via oral microbiota. However, few studies were employed to characterize the oral microbiota in hypertensive patients with periodontitis. Here, the present study profiled the oral microbiota in hypertensive participants with periodontitis. We found that the depleted abundance of nitrate-reducing bacteria and the enriched abundance of pathogens. Finally, we validated the role of Filifactor alocis in exacerbating HTN via infiltration of IFNγ[+] T cells in mice kidneys. Our study improved the understanding of oral microbiota linking PD and HTN.}, } @article {pmid40396732, year = {2025}, author = {Xin, T and Ye, Q and Hu, D}, title = {A relationship between body size and the gut microbiome suggests a conservation strategy.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0029425}, pmid = {40396732}, issn = {2165-0497}, support = {32370552//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; Feces/microbiology ; *Body Size ; *Felidae/microbiology/physiology ; *Conservation of Natural Resources ; Metagenome ; Clostridium/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Bacteroides/genetics/isolation & purification/classification ; Biodiversity ; }, abstract = {A key goal of conservation is to protect the biodiversity of wild species to support their continued evolution and survival. Conservation practice has long been guided by genetic, ecological, and demographic indicators of risk. Cope's rule suggests that species tend to evolve larger body sizes over time. Here, we provide strong evidence to support the inclusion of body size when formulating wildlife conservation strategies. The gut microbiome can mirror the physiological and environmental adaptation status of the host. This study established a connection between body size and the gut microbiome in the Felidae family using 70 fecal samples collected from 18 individuals through metagenomic data analysis and mining metagenome-assembled genomes (MAGs). Two enterotypes were identified in the Felidae gut: Bacteroides and Clostridium. Medium-sized felids predominantly harbored Clostridium, associated with pathogenicity, whereas large and small felids harbored both beneficial Bacteroides and pathogenic Clostridium. Species that evolved larger body sizes over time exhibited distinct changes in gut microbial communities, such as enhanced nutrient extraction and metabolic capabilities. Larger felids exhibited a more diverse, stable gut microbiome engaged in metabolic processes and extensive host interactions, indicating an evolved functional role in various biological processes. Conversely, that of smaller felids is less diverse, with more viruses and pathogenic elements primarily involved in chemical synthesis. These findings provide essential insights for developing conservation strategies that consider the nutritional needs of different-sized feline species, control the transmission of pathogens, and allocate resources based on their unique gut microbiome characteristics.IMPORTANCEBody size is a fundamental trait that varies greatly among taxa and has important implications for life history and ecology. Cope's rule suggests that species tend to evolve larger body sizes over time. However, its correlation to body size evolution remains unclear. This study aimed to establish a connection between body size and the gut microbiome in the Felidae family through metagenomic data analysis. Our results support Cope's rule, illustrating that increased body size correlates with shifts in the gut microbiome, enhancing survival and adaptability.}, } @article {pmid40396729, year = {2025}, author = {Cunningham, AL and Zhbannikov, IY and Myers, R and Tran, TH and Gao, W and Lemon, KP and Aquino, JN and Hurst, JH and Yoon, JW and Seed, PC and Kelly, MS}, title = {Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains.}, journal = {mSphere}, volume = {10}, number = {6}, pages = {e0025825}, pmid = {40396729}, issn = {2379-5042}, support = {K23 AI135090/AI/NIAID NIH HHS/United States ; R01 GM108494/GM/NIGMS NIH HHS/United States ; R21 AI154081/AI/NIAID NIH HHS/United States ; R35 GM141806/GM/NIGMS NIH HHS/United States ; }, mesh = {*Corynebacterium/genetics/metabolism/classification ; Humans ; *Genome, Bacterial ; *Biological Products/metabolism ; Multigene Family ; *Biosynthetic Pathways/genetics ; Genomics ; *Respiratory System/microbiology ; Microbiota ; Phylogeny ; }, abstract = {Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics.}, } @article {pmid40396204, year = {2025}, author = {Zöggeler, T and Kavallar, AM and Pollio, AR and Aldrian, D and Decristoforo, C and Scholl-Bürgi, S and Müller, T and Vogel, GF}, title = {Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2508951}, pmid = {40396204}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; *Pediatric Obesity/microbiology/complications ; *Fatty Liver/microbiology ; Male ; Metagenomics ; Female ; *Obesity/microbiology ; Adolescent ; Shotgun Sequencing ; }, abstract = {Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and without MASLD, MASH, and healthy controls. Electronic databases were searched for studies on the gut microbiome in children with obesity with/without MASLD or MASH, providing shotgun-metagenomic-sequencing data. Nine studies and an additionally recruited cohort were included. Fecal microbiomes of children with MASLD (n = 153) and MASH (n = 70) were significantly different in alpha- and beta-diversity (p < 0.001) compared to obese (n = 58) and healthy (n = 132). Species Faecalibacterium_prausnitzii and Prevotella_copri are differentially abundant between obese, MASLD and MASH groups. XGBoost and random forest-models accurately predict MASLD over obesity with an AUROC of 87% and MASH over MASLD with 89%. Pathway-abundance-based models accurately predict MASLD over obesity with an AUROC of 81% and MASH over MASLD with 88%. The composition of the gut microbiome is altered with increasing hepatic fibrosis and concomitant species-abundance increase of Prevotella_copri (p = 0.0082). Machine-learning models discriminate pediatric from adult MASH with an AUROC of 97%. The gut microbial composition is increasingly altered in children with the progression of MASLD toward MASH. This can be utilized as a fecal biomarker and highlights the impact of diet on the gut microbiome for disease intervention.}, } @article {pmid40393758, year = {2025}, author = {Jiang, JY and Fan, ZX and Yang, F and Liu, HM and Mao, M and Feng, L and Xiong, F and Li, P}, title = {[Composition of gut microbiota and characteristics of virulence factors genes in overweight or obese children and their relationship with liver metabolic inflammation].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {63}, number = {6}, pages = {642-648}, doi = {10.3760/cma.j.cn112140-20241128-00873}, pmid = {40393758}, issn = {0578-1310}, support = {2023YFS0034//Key R&D Project of Science and Technology Department of Sichuan Province/ ; }, mesh = {Humans ; Male ; Female ; Child ; *Gastrointestinal Microbiome/genetics ; *Virulence Factors/genetics ; Case-Control Studies ; *Pediatric Obesity/microbiology/metabolism ; *Overweight/microbiology/metabolism ; Feces/microbiology ; Inflammation/metabolism ; *Liver/metabolism ; *Obesity/microbiology ; Body Mass Index ; }, abstract = {Objective: To explore the composition of gut microbiome, the characteristics of virulence factor genes and their relationship with liver metabolic inflammation in overweight or obese children. Methods: A case-control design was conducted. From the children who visited the West China Second University Hospital of Sichuan University for medical or physical examinations between August 2021 and April 2022, a total of 23 obese children (obesity group), 8 overweight children (overweight group), and 22 healthy children (control group) were recruited. The body mass index of children was calculated after anthropometric measurements; metabolic inflammation indexes such as the levels of fasting blood glucose and hepatic function and renal function etc. were detected. The composition and abundance of gut microbiota in the feces of the children were detected by metagenomic sequencing technology and the Shannon index and Simpson index were calculated to assess the α diversity of virulence factor genes. The Wilcoxon rank-sum test was used for pairwise comparison between groups. The Spearman's rank correlation test was used for correlation analysis, and the Benjamini-Hochberg method was used to correct the P-value of multiple tests. Results: The obese group included 23 children aged 8.5 (6.3, 11.8) years, of whom 9 (39%) were male. The overweight group consisted of 8 children aged 9.2 (5.5, 12.3) years, of whom 4 were male. The control group comprised 22 children aged 5.3 (5.1, 5.4) years, of whom 10 (45%) were male. The obese group exhibited higher levels of alanine aminotransferase (ALT), gamma-glutamyl transferase (γ-GT), globulin, and uric acid compared to those of the control group (all P<0.05), with ALT also higher than that of the overweight group (P<0.05). The levels of fasting blood glucose, γ-GT, globulin, and uric acid in the overweight group were all higher than those in the control group (all P<0.05). The abundance of Coprococcus A (0.76 (0.00, 3.11) vs. 0.00 (0.00, 0.00), false discovery rate (FDR)<0.05) and Parasutterella (0.89 (0.08, 1.79) vs. 0.00 (0.00, 0.08), FDR<0.05) in the gut of children in the obese group were both higher than those of the control group. The number of virulence factor genes in the obese group was higher than those of the control group (941 (886, 977) vs. 890 (807, 920), P<0.05). The Simpson index and Shannon index of gut microbial virulence factor genes in the obese group were both higher than those of the control group (0.993 (0.992, 0.993) vs. 0.991(0.990, 0.991), (5.50 (5.46, 5.56) vs. 5.37 (5.30, 5.43), both P<0.01). The abundance of gut microbiota virulence factors genes all showed positive correlations with fasting blood glucose, ALT, γ-GT, and uric acid levels in children (all r>0.3, all FDR<0.05). The abundance of 17 gut microbial virulence factor genes were all positively associated with γ-GT levels (all r>0.3, all FDR<0.05). The virulence factor genes (LpxH, LpxB, LpxK) of lipopolysaccharide were all positively correlated with plasma γ-GT and globulin levels (all r>0.3, all FDR<0.05). Conclusions: Overweight or obese children exhibited elevated liver metabolic-inflammatory markers compared to their normal-weight counterparts. Notably, obese children demonstrated gut microbiota dysbiosis accompanied by enrichment of virulence factor genes, which may promote liver metabolic inflammation through pathways such as lipopolysaccharide biosynthesis.}, } @article {pmid40392941, year = {2025}, author = {Feng, C and Liang, Z and Liao, X and Lin, K and Zhai, Y and Liu, G and Malpei, F and Hu, A}, title = {Microbial Dynamics on Different Microplastics in Coastal Urban Aquatic Ecosystems: The Critical Roles of Extracellular Polymeric Substances.}, journal = {Environmental science & technology}, volume = {59}, number = {21}, pages = {10554-10566}, pmid = {40392941}, issn = {1520-5851}, mesh = {*Microplastics ; Ecosystem ; Extracellular Polymeric Substance Matrix ; Bacteria ; Water Pollutants, Chemical ; Microbiota ; }, abstract = {Microplastics (MPs) serve as carriers for microbial community colonization, forming unique ecosystems known as plastispheres in urban aquatic ecosystems. However, interactions among microbes, extracellular polymeric substances (EPS), and MPs remain poorly understood. This study investigates microbial consortia and their EPS secretion behaviors across various plastispheres at two representative coastal urban water sites. Permutational multivariate analysis of variance revealed that MP type significantly influenced microbial community structures in reservoir environments (R[2] = 0.60, p < 0.001), highlighting the pronounced impact of MP types in high-quality urban waters. Specific microbial phyla and genera were identified as key contributors to EPS compositional variations across different plastispheres. Hierarchical partitioning results identified Acidobacteria, Nitrospirae, and Planctomycetes as influential phyla positively affecting EPS composition. Spearman correlation analysis pinpointed Robiginitialea (positive correlation) and Fimbriiglobus (negative correlation) as critical genera influencing EPS dynamics. Moreover, EPS-related gene abundance corresponded closely with observed EPS compositional differences. Dominant genes associated with protein biosynthesis included xapD in reservoirs and glnA in bays, while glmS and eno were predominant for polysaccharide biosynthesis in bays. This research advances our understanding of microbial-EPS-MP interactions in urban water systems, offering critical insights into ecological remediation and risk assessment of MP pollution.}, } @article {pmid40392071, year = {2025}, author = {You, Q and Wang, K and Zhao, Z and Zhou, H and Lan, Z and Liang, H and Deng, R and Li, W and Shen, S and Wang, R and Zhang, K and Zheng, D and Sun, J}, title = {Reduction of Bacteroides fragilis in Gut Microbiome of Chronic Hepatitis B Patients Promotes Liver Injury.}, journal = {Journal of medical virology}, volume = {97}, number = {5}, pages = {e70395}, doi = {10.1002/jmv.70395}, pmid = {40392071}, issn = {1096-9071}, support = {//This study was supported by the Guangzhou Science and Technology Plan Project (Grant 2024B03J0326), the Guangdong Basic and Applied Basic Research Foundation of Guangzhou Joint Fund (Grant 2022B1515120039), the National Natural Science Foundation of China (Grant U22A20274), and the Guangdong Basic and Applied Basic Research Foundation (Grant 2023A1515010437)./ ; }, mesh = {Humans ; *Bacteroides fragilis/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Hepatitis B, Chronic/microbiology/complications/pathology ; Male ; Female ; Adult ; Case-Control Studies ; Animals ; Middle Aged ; Mice ; Liver/pathology ; Alanine Transaminase/blood ; Metagenomics ; Disease Models, Animal ; }, abstract = {In chronic hepatitis B (CHB) patients under antiviral treatment, liver injury, as evidenced by elevated alanine transaminase (ALT), is associated with unfavorable outcomes and needs effective treatment. The interaction between gut microbiota and liver injury in CHB patients remains unclear. Using a case-control design, 28 cases with elevated ALT and 28 matched controls with normal ALT were randomly selected from CHB patients with viral control. Clinical characteristics were comparable between groups. Metagenomic sequencing revealed that Bacteroides fragilis was decreased in cases and exhibited the greatest disparity between cases and controls. Mice colonized by gut microbiota from cases exhibited more severe liver damage in both LPS-induced and MCD diet-induced liver injury models, and had a lower abundance of B. fragilis compared to mice colonized by gut microbiota from controls. Oral gavage of B. fragilis improved both LPS-induced and MCD diet-induced liver injury. Metabolomics analysis revealed that the levels of 7-Ketolithocholic acid (7-Keto-LCA) were positively correlated with B. fragilis and significantly increased in the cultural supernatant of B. fragilis. Consistently, 7-Keto-LCA exerted protective effects against both LPS-induced and MCD diet-induced liver damage. Targeting gut microbiota might be a promising therapeutic treatment for alleviation residual liver inflammation in CHB patients with viral control.}, } @article {pmid40391895, year = {2025}, author = {Hillege, LE and Trepka, KR and Guthrie, BGH and Fu, X and Aarnoutse, R and Paymar, MR and Olson, C and Zhang, C and Ortega, E and Ramirez, L and de Vos-Geelen, J and Valkenburg-van Iersel, L and van Hellemond, IEG and Baars, A and Vestjens, JHMJ and Penders, J and Deutschbauer, A and Atreya, CE and Kidder, WA and Smidt, ML and Ziemons, J and Turnbaugh, PJ}, title = {Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity.}, journal = {mBio}, volume = {16}, number = {6}, pages = {e0093025}, pmid = {40391895}, issn = {2150-7511}, support = {R01HL122593/HL/NHLBI NIH HHS/United States ; R01 CA255116/CA/NCI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01CA255116/CA/NCI NIH HHS/United States ; 58-8050-3-003//U.S. Department of Agriculture/ ; R01DK114034/DK/NIDDK NIH HHS/United States ; T32 GM141323/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; *Capecitabine/adverse effects/therapeutic use ; *Vitamin K 2/metabolism ; Feces/microbiology/chemistry ; *Antineoplastic Agents/adverse effects/therapeutic use ; Female ; Male ; *Vitamins/biosynthesis ; Escherichia coli/drug effects/metabolism/genetics ; Bacteria/metabolism/genetics/drug effects ; Middle Aged ; Metagenomics ; }, abstract = {Dose-limiting toxicities pose a major barrier to cancer treatment. While preclinical studies show that the gut microbiota influences and is influenced by anticancer drugs, data from patients paired with careful side effect monitoring remains limited. Here, we investigate capecitabine (CAP)-microbiome interactions through longitudinal metagenomic sequencing of stool from 56 advanced colorectal cancer patients. CAP significantly altered the gut microbiome, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation revealed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Stool menaquinol gene and metabolite levels were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted toxicities in an independent cohort. Taken together, these results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells. Further, our findings provide a foundation for in-depth mechanistic dissection, human intervention studies, and extension to other cancer treatments.IMPORTANCESide effects are common during the treatment of cancer. The trillions of microbes found within the human gut are sensitive to anticancer drugs, but the effects of treatment-induced shifts in gut microbes for side effects remain poorly understood. We profiled gut microbes in colorectal cancer patients treated with capecitabine and carefully monitored side effects. We observed a marked expansion in genes for producing vitamin K2 (menaquinone). Vitamin K2 rescued gut bacterial growth and was associated with decreased side effects in patients. We then used information about gut microbes to develop a predictive model of drug toxicity that was validated in an independent cohort. These results suggest that treatment-associated increases in bacterial vitamin production protect both bacteria and host cells from drug toxicity, providing new opportunities for intervention and motivating the need to better understand how dietary intake and bacterial production of micronutrients like vitamin K2 influence cancer treatment outcomes.}, } @article {pmid40391128, year = {2025}, author = {Yatera, K and Wang, Z and Shibata, Y and Ishikawa, N and Homma, T and Fukushima, K and Hataji, O and Inoue, Y and Kawabata, H and Miki, K and Sato, K and Tobino, K and Yoshida, M and Ishii, T and Ito, R and Kobayashi, T and Kawamatsu, S and Compton, CH and Jones, PW}, title = {Sputum Microbiome, Potentially Pathogenic Organisms, and Clinical Outcomes in Japanese Patients with COPD and Moderate Airflow Limitation: The Prospective AERIS-J Study.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {20}, number = {}, pages = {1477-1492}, pmid = {40391128}, issn = {1178-2005}, mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; *Bacteria/pathogenicity/genetics/isolation & purification ; Disease Progression ; Forced Expiratory Volume ; Japan/epidemiology ; *Lung/microbiology/physiopathology ; *Microbiota ; Prospective Studies ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Severity of Illness Index ; *Sputum/microbiology ; East Asian People ; }, abstract = {BACKGROUND: In Western studies, lung microbiome changes are reported in patients with chronic obstructive pulmonary disease (COPD) and are associated with poorer outcomes, but similar studies in Asian patients or those with less severe COPD are limited.

METHODS: The Acute Exacerbation and Respiratory InfectionS in COPD Japan (AERIS-J; jRCT1080224632/NCT03957577) was a prospective, non-interventional study to evaluate sputum microbiome diversity at baseline and after 12 months (V2; exploratory analysis), in patients aged 40-80 years with stable COPD (June 2019-June 2022). Baseline sputum potentially pathogenic organisms (PPOs) were identified. Blood cell counts and COPD Assessment Test (CAT) scores were collected at baseline and COPD symptoms measured over 12 months using the Evaluating Respiratory Symptoms in COPD and EXAcerbations of Chronic pulmonary disease Tool, collected by eDiary.

RESULTS: Patients (N=63) had a mean age of 72.8 years, and percent predicted post-bronchodilator forced expiratory volume in 1 second was 58.3%; 92% were male. Across 62 baseline sputum samples, microbiome composition was similar between 16S rRNA/metagenomic datasets. Patients graded Global Initiative for Chronic Obstructive Lung Disease (GOLD) III versus GOLD I/II had minimal differences in their microbial taxonomic profile and no differences in microbial diversity (Wilcoxon P=0.71). Alpha diversity (Shannon index) positively correlated with blood basophils (rho=0.41; P=0.0019) and negatively correlated with CAT score (rho=0.36; P=0.0069). Alpha diversity and sputum (rho: -0.0637; P=0.7836) or blood (rho: 0.1739; P=0.2043) eosinophils were not correlated. No difference in alpha (P=0.5) or beta (P=0.3) diversity or Operational Taxonomic Unit (Anosim R=-0.024; P=0.892) was observed between PPO-positive or -negative sputum.

CONCLUSION: A less diverse microbiome correlated with poorer health status and lower blood basophils in patients with COPD and moderate airflow limitation. There was no relationship between PPO presence and microbiome diversity.}, } @article {pmid40390177, year = {2025}, author = {Ren, Z and Wang, M and Yu, J and Zhang, L and Lin, Z and Li, X and Zhang, Y}, title = {Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70110}, doi = {10.1111/1462-2920.70110}, pmid = {40390177}, issn = {1462-2920}, support = {42301132//National Natural Science Foundation of China/ ; NKL2023-QN02//Key Laboratory of Lake and Watershed Science for Water Security/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation & purification ; *Lakes/microbiology ; Phylogeny ; Biodiversity ; Tibet ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai-Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon index) generally decreased with depth. Euryarchaeota was the most abundant phylum, though its relative abundance declined with depth, while Thaumarchaeota increased. At the order level, Methanosarcinales and Nitrosopumilales showed increased relative abundance with depth, indicating adaptation to deeper anoxic layers, whereas Methanomicrobiales and Methanotrichales decreased. Beta diversity increased with depth, shifting from stochastic to deterministic processes. Network topology revealed reduced species connectivity but heightened modularity at depth, signalling niche specialisation. Functionally, genes associated with the initial steps of methane metabolism (Fwd, Mtd, Mer) increased with depth, while those involved in later steps (Mtr, Mcr) decreased, suggesting reduced energy conservation efficiency and lower overall methanogenesis rates in deeper sediments. These findings highlight the significant impact of vertical stratification on archaeal community structure, interaction networks, and functional capabilities.}, } @article {pmid40390128, year = {2025}, author = {Liao, H and Wen, C and Huang, D and Liu, C and Gao, T and Du, Q and Yang, QE and Jin, L and Ju, F and Yuan, MM and Tang, X and Yu, P and Zhou, S and Alvarez, PJ and Friman, VP}, title = {Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {127}, pmid = {40390128}, issn = {2049-2618}, support = {42277357//National Natural Science Foundation of China/ ; }, mesh = {*Streptomyces/virology/genetics/drug effects ; *Soil Microbiology ; *Bacteriophages/physiology/genetics ; Metagenomics/methods ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; China ; *Drug Resistance, Bacterial/genetics ; Sewage/virology ; }, abstract = {BACKGROUND: Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.

RESULTS: Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.

CONCLUSION: Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.}, } @article {pmid40390033, year = {2025}, author = {Teng, T and Huang, F and Xu, M and Li, X and Zhang, L and Yin, B and Cai, Y and Chen, F and Zhang, L and Zhang, J and Geng, A and Chen, C and Yu, X and Sui, J and Zhu, ZJ and Guo, K and Zhang, C and Zhou, X}, title = {Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {128}, pmid = {40390033}, issn = {2049-2618}, support = {82301714//the National Natural Science Foundation of China/ ; 22425404//the National Natural Science Foundation of China/ ; 82271565//the National Natural Science Foundation of China/ ; 2023TQ0398//the China Postdoctoral Science Foundation/ ; CSTB2023NSCQ-BHX0106//Natural Science Foundation of Chongqing, China/ ; 2208013341918508//Postdoctoral Innovation Talents Support Program of Chongqing, China/ ; 2022YFC3400702//National Key R&D Program of China/ ; 2024YFC2707800//National Key R&D Program of China/ ; 2022ZD0212900//STI2030-Major Projects/ ; }, mesh = {Humans ; Adolescent ; Child ; *Gastrointestinal Microbiome/physiology ; Male ; *Depressive Disorder, Major/microbiology/metabolism ; Female ; *Amino Acids/deficiency/blood/metabolism ; Magnetic Resonance Imaging ; Animals ; Rats ; Brain/diagnostic imaging/metabolism ; Feces/microbiology ; Metagenomics/methods ; Metabolomics/methods ; *Depression/microbiology ; }, abstract = {BACKGROUND: Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.

RESULTS: We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value < 0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value = 0.001, M[2] = 0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.

CONCLUSIONS: Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.}, } @article {pmid40389724, year = {2025}, author = {Yang, M and Qi, Y and Gao, P and Li, L and Guo, J and Zhao, Y and Liu, J and Chen, Z and Yu, L}, title = {Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {766}, pmid = {40389724}, issn = {2399-3642}, support = {202449CE340009, 202201AU070043, 202101BA070001-174//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 202501AU070008//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 2025J0753//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; 2023J0827//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; }, mesh = {*Endophytes/physiology ; *Plant Diseases/microbiology ; *Amorphophallus/microbiology ; *Microbiota ; *Disease Resistance ; *Adaptation, Physiological ; Stress, Physiological ; *Bacteria ; }, abstract = {Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.}, } @article {pmid40389466, year = {2025}, author = {Salehi, M and Laitinen, V and Bhanushali, S and Bengtsson-Palme, J and Collignon, P and Beggs, JJ and Pärnänen, K and Lahti, L}, title = {Gender differences in global antimicrobial resistance.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {79}, pmid = {40389466}, issn = {2055-5008}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 330887//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 348439//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 20220114//Alhopuro Foundation/ ; 20220114//Alhopuro Foundation/ ; 2019-00299//Swedish Research Council/ ; FFL21-0174//Swedish Foundation for Strategic Research/ ; KAW 2020.0239//Data-Driven Life Science/ ; }, mesh = {Humans ; Female ; Male ; Sex Factors ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Adult ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Global Health ; Middle Aged ; }, abstract = {Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.}, } @article {pmid40388589, year = {2025}, author = {Lei, Z and Wang, H and Zhang, H and Liu, W and He, Z and Wang, Z and Zhang, H and Wang, Y and Tang, Y and Hu, C and Zhao, X}, title = {Sultr1;2-Mediated Recruitment of Selenium-Oxidizing Bacteria Promotes Plant Selenium Uptake.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {22}, pages = {13313-13326}, doi = {10.1021/acs.jafc.5c01540}, pmid = {40388589}, issn = {1520-5118}, mesh = {*Selenium/metabolism ; *Solanum lycopersicum/metabolism/microbiology/genetics/growth & development ; Oxidation-Reduction ; Soil Microbiology ; *Methylobacterium/metabolism/genetics/isolation & purification ; *Bacterial Proteins/metabolism/genetics ; Plant Roots/microbiology/metabolism ; Soil/chemistry ; Microbiota ; }, abstract = {Plants can shape their root microbiome to promote growth and selenium uptake. Here, we used metagenomics, 16S high-throughput sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics assays to investigate the role of Sultr1;2, which is the major selenium transporter gene, in recruiting microbial communities to regulate soil selenium bioavailability and plant selenium uptake. Results shows that the overexpression of Sultr1;2 in tomato significantly enriched Methylobacterium genus. The isolated strains of Methylobacterium possess multiple plant-growth-promoting functions and selenium oxidation capability and inoculation with these strains increases soil selenium availability. The upregulated metabolites of Sultr1;2-overexpressing tomato were significantly enriched in the arginine and proline metabolism pathway. The key upregulated metabolites significantly improved the growth rate and selenium-oxidizing ability of Methylobacterium strains, and the combined addition of key upregulated metabolites and synthetic microbial community significantly increased soil selenium bioavailability and plant selenium uptake. This study provides insights into leveraging plant genetic engineering to identify key functional microbial communities for sustainable selenium-rich agricultural development.}, } @article {pmid40388544, year = {2025}, author = {Kohnert, E and Kreutz, C}, title = {Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0321452}, pmid = {40388544}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Benchmarking ; Computer Simulation ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; }, abstract = {Differential abundance (DA) analysis of metagenomic microbiome data is essential for understanding microbial community dynamics across various environments and hosts. Identifying microorganisms that differ significantly in abundance between conditions (e.g., health vs. disease) is crucial for insights into environmental adaptations, disease development, and host health. However, the statistical interpretation of microbiome data is challenged by inherent sparsity and compositional nature, necessitating tailored DA methods. This benchmarking study aims to simulate synthetic 16S microbiome data using metaSPARSim (Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B. MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. Available from: https://doi.org/10.1101/2023.03.23.533996), and sparseDOSSA2 (Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, et al. A statistical model for describing and simulating microbial community profiles. PLOS Comput Biol. 2021;17(9):e1008913. https://doi.org/10.1371/journal.pcbi.1008913 PMID: 34516542) , leveraging 38 real-world experimental templates (S3 Table) previously utilized in a benchmark study comparing DA tools. These datasets, drawn from diverse environments such as human gut, soil, and marine habitats, serve as the foundation for our simulation efforts. We employ the same 14 DA tests that were previously used with the same experimental data in benchmark studies alongside 8 DA tests that were developed subsequently. Initially, we will generate synthetic data closely mirroring the experimental datasets, incorporating a known truth to cover a broad range of real-world data characteristics. This approach allows us to assess the ability of DA methods to recover known true differential abundances. We will further simulate datasets by altering sparsity, effect size, and sample size, thus creating a comprehensive collection for applying the 22 DA tests. The outcomes, focusing on sensitivities and specificities, will provide insights into the performance of DA tests and their dependencies on sparsity, effect size, and sample size. Additionally, we will calculate data characteristics (S1 and S2 Table) for each simulated dataset and use a multiple regression to identify informative data characteristics influencing test performance. Our prior study, where we used simulated data without incorporating a known truth, demonstrated the feasibility of using synthetic data to validate experimental findings. This current study aims to enhance our understanding by systematically evaluating the impact of known truth incorporation on DA test performance, thereby providing further information for the selection and application of DA methods in microbiome research.}, } @article {pmid40388308, year = {2025}, author = {Wang, S and Kong, F and Dai, D and Li, C and Hao, Y and Wang, E and Cao, Z and Wang, Y and Wang, W and Li, S}, title = {Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40388308}, issn = {2047-217X}, support = {2022YFD1301400//National Key Research and Development Program/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Female ; *Peripartum Period/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Pregnancy ; }, abstract = {BACKGROUND: Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.

RESULTS: In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.

CONCLUSIONS: Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.}, } @article {pmid40387602, year = {2025}, author = {Bonacolta, AM and Krause-Massaguer, J and Unuma, T and Del Campo, J}, title = {The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.}, journal = {The Journal of eukaryotic microbiology}, volume = {72}, number = {3}, pages = {e70013}, pmid = {40387602}, issn = {1550-7408}, support = {//University of Miami/ ; PID2020-118836GA-I00//Ministerio de Ciencia, Innovación y Universidades/ ; 2021 SGR 00420//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; }, mesh = {Animals ; Phylogeny ; *Sea Cucumbers/parasitology ; *Apicomplexa/genetics/classification/isolation & purification ; Host Specificity ; Female ; Host-Parasite Interactions ; Genome, Mitochondrial ; }, abstract = {Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.}, } @article {pmid40387372, year = {2025}, author = {Lei, Z and Zhang, H and Liu, W and Sheng, J and Zhang, H and Wang, Y and Tang, Y and Wang, H and Ding, C and Qiao, W and Zhu, Y and Yang, G and Zhang, Y and Liu, Z and Zhou, N and Hu, C and Zhao, X}, title = {Dynamic and Stable Core Microbiota Assist Plants in Enriching Selenium and Reducing Cadmium Absorption.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {25}, pages = {e00862}, pmid = {40387372}, issn = {2198-3844}, support = {2023YFD1900904//National Key Research and Development Program of China/ ; SKLEG2024225//State Key Laboratory of Environmental Geochemical/ ; 23567601H//State Key Laboratory of North China Crop Improvement and Regulation, S&T Program of Hebei/ ; 24XJTRZW13//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; WY22B04//Wuhan Municipal Health Commission/ ; Grants KJ2025-5//2025 Science and Technology Project of Hubei Geological Bureau/ ; Grants 2023AFD215//Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China/ ; D20234501//Science and Technology Research Project of Hubei Province/ ; 23xjz05R//Hubei Polytechnic University/ ; }, mesh = {*Selenium/metabolism ; *Cadmium/metabolism ; Rhizosphere ; *Microbiota/physiology/genetics ; Soil Microbiology ; *Brassica napus/metabolism/microbiology ; Soil/chemistry ; Plant Roots/metabolism/microbiology ; Metagenomics ; }, abstract = {Rhizosphere microbiome is crucial for regulating rhizosphere complex nutrient dynamics. However, mechanisms by which plants regulate rhizosphere microbes to manage nutrient availability under coexisting beneficial and harmful elements remain unclear. This study focuses on the rhizosphere microbiome of Brassica napus in different naturally selenium (Se)-cadmium (Cd)-rich soils, the functionality of this rhizosphere, and the changes in the availability of rhizosphere nutrients. Microbiome analysis, metagenomics, genomic analysis, strain isolation, and functional validation are performed to investigate these relationships. Results show that a significant negative correlation is observed between the rhizosphere available Se and Cd content across the plant whole growth cycle and identified a group of core microbiota that are highly positively correlated with available Se and negatively correlated with available Cd. Genomics and metagenomics analyses reveal that the core microbiota has a higher substrate preference for amino acids related to the glutathione metabolic pathway. Key glutathione-related-amino acids and synthetic microbial community significantly improve the expression of glutathione anabolism and related amino acid transport genes and enhance Se uptake and reduce Cd absorption in plants grown in various Se-Cd-rich soils. This study provides insights into the mechanisms of root-associated microbes responding to complex soil nutrients during plant growth.}, } @article {pmid40383397, year = {2025}, author = {Merrick, B and Prossomariti, D and Allen, E and Bisnauthsing, K and Kertanegara, M and Sergaki, C and Le Guennec, AD and Delord, M and Bell, JT and Conte, MR and Moyes, DL and Shankar-Hari, M and Douiri, A and Goodman, AL and Shawcross, DL and Goldenberg, SD}, title = {Faecal microbiota transplant to ERadicate gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO): A feasibility randomised controlled trial.}, journal = {The Journal of infection}, volume = {91}, number = {1}, pages = {106504}, doi = {10.1016/j.jinf.2025.106504}, pmid = {40383397}, issn = {1532-2742}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods/adverse effects ; Male ; Female ; Middle Aged ; Feasibility Studies ; *Carrier State/therapy/microbiology ; Aged ; Adult ; *Gastrointestinal Tract/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome ; Drug Resistance, Multiple, Bacterial ; Treatment Outcome ; Anti-Bacterial Agents ; *Enterobacteriaceae Infections/therapy/microbiology ; }, abstract = {OBJECTIVES: The gastrointestinal tract (GIT) is a reservoir of multidrug-resistant organisms (MDRO). Colonisation with MDRO precedes invasive infections, which can be challenging to treat with excess morbidity and mortality compared to antimicrobial-susceptible infections. Currently, there are no effective GIT decolonisation strategies. Whilst faecal microbiota transplant (FMT) has emerged as a potential therapeutic, there remains uncertainty about its feasibility, safety, and efficacy.

METHODS: Population: Patients with invasive infection with extended-spectrum beta-lactamase (ESBL-) or carbapenem-resistant Enterobacterales (CRE) and persistent GIT carriage.

INTERVENTION: Three doses of encapsulated lyophilised FMT.

COMPARATOR: Matched placebo capsules.

OUTCOMES: Primary outcome was participant consent rate as a proportion of those approached to be screened for GIT carriage of ESBL-E/CRE. Secondary outcomes were additional feasibility, safety and tolerability, and efficacy metrics. Exploratory outcomes included stool metagenomic analysis.

RESULTS: Of 460 approached individuals, 124 (27%) consented. 53/124 participants (43%) fulfilled all eligibility criteria. 44/53 (83%) of those eligible were randomised and 41/44 (93%) received investigational medicinal product (IMP): 20 FMT and 21 placebo. 39/41 (95%) completed IMP dosing. Abdominal bloating and skin and subcutaneous tissue disorders were more common following FMT, but there were no unanticipated harms. MDRO carriage decreased over time across arms but was lower at all time points in the FMT arm. FMT increased microbiome diversity and microbiome-based health measures. FMT recipients' samples clustered into two groups, with those with more dissimilar community composition to donors more likely to decolonise post-FMT (3/5 vs. 0/12, p = 0.01). Patients that decolonised exhibited a trend towards increased proportional representation of donor-derived strains in their post-FMT samples (p = 0.05) and change in strain dominance within MDRO at the species-level.

CONCLUSIONS: Progression to a substantive trial is feasible with modifications to the existing FERARO protocol. FMT was safe, well tolerated, and acceptable to patients colonised with MDRO. Microbiome analysis infers that greater donor-recipient microbiome dissimilarity at baseline and higher rates of donor-derived strain engraftment favour MDRO decolonisation, which in turn maybe facilitated by conspecific strain replacement.}, } @article {pmid40382475, year = {2025}, author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG}, title = {The Microbial Ecology of Antarctic Sponges.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {44}, pmid = {40382475}, issn = {1432-184X}, mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Ecosystem ; Fungi/classification/genetics/isolation & purification ; }, abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.}, } @article {pmid40382365, year = {2025}, author = {Schilling, M and Jagdev, M and Thomas, H and Johnson, N}, title = {Metagenomic analysis of mosquitoes from Kangerlussuaq, Greenland reveals a unique virome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17141}, pmid = {40382365}, issn = {2045-2322}, mesh = {Animals ; Greenland ; *Virome/genetics ; *Metagenomics/methods ; *Aedes/virology/genetics ; *Mosquito Vectors/virology ; Metagenome ; Phylogeny ; *Culicidae/virology ; Climate Change ; }, abstract = {Climate change is dramatically affecting vector ecology in extreme environments such as the Arctic. However, little is known about the current status of viruses of arthropod vectors located in such northerly locations. As part of a field survey on the role of wildlife in international movement of zoonotic pathogens, we sampled mammalophilic mosquitoes near the settlement of Kangerlussuaq, Greenland in July 2022 and July 2023 to investigate their virome. The majority of mosquitoes were identified as either Aedes impiger or Aedes nigripes. Metagenomic analysis of RNA extracted from species pools detected a number of novel RNA viruses belonging to a range of different virus families, including Flaviviridae, Orthomyxoviridae, Bunyavirales, Totiviridae and Rhabdoviridae. However, the sequence identities when compared to previously published, were as low as 34% at the amino acid level. Furthermore, a comparison of virome diversity between Aedes species emphasises the uniqueness of both Aedes impiger and Aedes nigripes from this secluded ecosystem. It also highlights the need to better understand the viromes of potential pathogen vectors as the impacts of climate change are experienced in such northerly ecosystems.}, } @article {pmid40382068, year = {2025}, author = {Zhang, Z and Ran, X and Guo, Z and Hou, Q and Qu, D and Wang, C and Xu, Y and Wang, Y}, title = {Microbial diversity, functional properties, and flavor characteristics of high-temperature Daqu with different colors.}, journal = {Food research international (Ottawa, Ont.)}, volume = {212}, number = {}, pages = {116406}, doi = {10.1016/j.foodres.2025.116406}, pmid = {40382068}, issn = {1873-7145}, mesh = {Color ; *Taste ; *Food Microbiology ; *Hot Temperature ; Odorants/analysis ; Humans ; *Bacteria/classification/genetics ; *Microbiota ; China ; }, abstract = {High-temperature Daqu (HTD) plays a crucial role in the quality of sauce-flavor baijiu. Daqu of different colors serves distinct functions in the baijiu brewing process. However, indicators for distinguishing among different-colored Daqu remain insufficient. This study investigated the microbial community structures, physicochemical properties, and E-sensory characteristics of different-colored HTD from Shandong Province. The results revealed significant differences in microbial communities among the three HTD types (P < 0.05). Kroppenstedtia eburnea, three Bacillus species, and Weizmannia coagulans were significantly enriched in white Daqu; an unclassified Staphylococcus species dominated in black Daqu; and Aspergillus oryzae, Aspergillus fumigatus, and Proteus mirabilis were highly abundant in yellow Daqu. Compared to HTD from Guizhou and Hubei, Shandong HTD was characterized by microbial species such as Proteus mirabilis and Bacillus velezensis. Using metagenomic analysis, we, for the first time, identified Thermomyces lanuginosus, Lentibacillus daqui, and an unclassified Thermoascus species as potential major contributors to pyrazine synthesis in HTD. The primary differences among the three colored Shandong Daqu types lay in their aroma profiles rather than taste. Electronic nose and electronic tongue analyses demonstrated that the W6S and W3S sensors effectively distinguished black and white Daqu, respectively, marking a novel application of these technologies in Daqu analysis. Acidity was identified as a key factor influencing microbial community structure, flavor characteristics, and enzyme activities, with a nonlinear relationship observed between acidity and enzyme activities. This study highlights the microbial and sensory distinctions among different-colored HTD and provides effective indicators for distinguishing these three types of Daqu.}, } @article {pmid40381442, year = {2025}, author = {Zhang, X and Li, M and Xiao, Y and Yang, X and Zhou, H and Qu, Y and Zhan, J}, title = {Metagenomics reveals combined effects of microplastics and antibiotics on microbial community structure and function in coastal sediments.}, journal = {Marine pollution bulletin}, volume = {218}, number = {}, pages = {118153}, doi = {10.1016/j.marpolbul.2025.118153}, pmid = {40381442}, issn = {1879-3363}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Anti-Bacterial Agents/toxicity ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Metagenomics ; *Microbiota/drug effects ; Bacteria/drug effects ; }, abstract = {Microplastics and antibiotics are emerging pollutants in marine environments, yet their combined effects on coastal sediments remain poorly understood. This study examined the impacts of microplastics and antibiotics on sediment properties and microbial communities through a 60-day laboratory simulation. Results showed that microplastics significantly reduced carbon, nitrogen, and phosphorus levels in sediments, while both antibiotics and combined pollution decreased phosphorus content. Combined pollution also increased NH4[+]-N concentration. Enzyme activity analysis revealed that microplastics elevated alkaline phosphatase activity, antibiotics increased fluorescein diacetate (FDA) hydrolase activity but decreased urease activity, and their combination further enhanced FDA hydrolase activity. Metagenomics analysis demonstrated that the presence of microplastics and antibiotics altered microbial community structure and metabolic functions. The dominant phylum Pseudomonadota (42.62 %-56.24 %) showed reduced abundance under combined pollution. Antibiotics significantly increased resistance gene abundance, while combined pollution led to selective enrichment of these genes. Both pollutants inhibited ammonia assimilation, and antibiotics also suppressed dissimilatory nitrate reduction. Conversely, combined pollution promoted nitrification and nitrogen fixation. While microplastics and antibiotics inhibited methane synthesis, combined pollution increased methane production via elevated mttB and hdrA genes. Antibiotics also reduced methane-oxidizing bacteria and genes, suppressing methane oxidation. These findings provide crucial insights into the ecological impacts of microplastics and antibiotics on coastal sediments, offering a theoretical basis for future marine pollution management strategies.}, } @article {pmid40380272, year = {2025}, author = {Zhang, S and Zheng, N and Zhao, S and Wang, J}, title = {Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {124}, pmid = {40380272}, issn = {2049-2618}, support = {2023M743835//Project Funded by China Postdoctoral Science Foundation/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 2022YFD1301000//National Key Research and Development Program of China/ ; 2004DA125184G2406//State Key Laboratory of Animal Nutrition and Feeding/ ; }, mesh = {Animals ; *Sulfinic Acids/pharmacology/chemistry ; *Urease/antagonists & inhibitors/metabolism/chemistry ; *Rumen/microbiology ; *Urea/metabolism ; Disulfides/pharmacology ; *Nitrogen/metabolism ; Cattle ; Molecular Docking Simulation ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/drug effects/classification/genetics ; Enzyme Inhibitors/pharmacology ; }, abstract = {BACKGROUND: Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and [15]N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.

RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77 ± 1.21 μM. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A [15]N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.

CONCLUSION: Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.}, } @article {pmid40378832, year = {2025}, author = {Sarhan, MS and Antonello, G and Weissensteiner, H and Mengoni, C and Mascalzoni, D and Waldron, L and Segata, N and Fuchsberger, C}, title = {Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?.}, journal = {Cell}, volume = {188}, number = {10}, pages = {2561-2566}, doi = {10.1016/j.cell.2025.03.023}, pmid = {40378832}, issn = {1097-4172}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Metagenome ; *Metagenomics/ethics ; Privacy ; Microbiota ; *Genetic Privacy/ethics ; }, abstract = {Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.}, } @article {pmid40378749, year = {2025}, author = {Yu, YL and Lin, WH and Surampalli, RY and Chen, SC and Kao, CM}, title = {Adaptive fluoride removal across concentration scales: Potential roles of microbial and acicular gypsum interactions in nitrogen and phosphate cycling.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138628}, doi = {10.1016/j.jhazmat.2025.138628}, pmid = {40378749}, issn = {1873-3336}, mesh = {*Calcium Sulfate/chemistry ; *Fluorides/chemistry ; *Phosphates/metabolism/chemistry ; *Nitrogen/metabolism/chemistry ; *Water Pollutants, Chemical/chemistry/metabolism ; Groundwater/chemistry ; Microbiota ; Bacteria/metabolism/genetics ; }, abstract = {Fluoride contamination in groundwater is a critical environmental and public health concern. Traditional remediation methods, including chemical precipitation and adsorption, are hindered by low nucleation efficiency at low fluoride concentrations and severe microbial inhibition under high fluoride stress. This study introduces an adaptive two-stage remediation system that synergistically integrates abiotic and biotic mechanisms to achieve effective fluoride removal across concentration scales. In Stage I, under elevated fluoride stress (100 mg/L), acicular gypsum (AG) facilitated abiotic calcium precipitation, effectively reducing fluoride toxicity and creating favorable conditions for microbial activity. Residual calcium released from AG further supported microbial-induced calcium precipitation (MICP) in Stage II under lower fluoride stress (10 mg/L). The system achieved a fluoride removal efficiency of 98.85 % under high fluoride conditions and demonstrated consistent performance across a broad concentration range. This integrated approach, combining abiotic and biotic mechanisms, offers a promising strategy for addressing diverse fluoride contamination scenarios. Here, phosphate (P)-mediated mineralization and microbial denitrification drive pH modulation, stabilizing fluoride as fluorapatite [Ca5(PO4)3F]. Microbial community and network analysis revealed key taxa, including Cupriavidus and Ralstonia, which facilitated P cycling and fluorapatite formation. Additionally, Bradyrhizobium enhanced nitrogen (N) cycling and supported early microbial adaptation, emphasizing the interplay of microbial interactions in driving system functionality. Functional predictions using PICRUSt2 identified genes associated with N and P cycling, highlighting the capacity of the system for nutrient adaptation under complex environmental conditions.}, } @article {pmid40378468, year = {2025}, author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW}, title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.}, journal = {Water research}, volume = {283}, number = {}, pages = {123683}, doi = {10.1016/j.watres.2025.123683}, pmid = {40378468}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Planktothrix ; Biomarkers ; Microbiota ; Nitrogen/metabolism ; Cyanobacteria ; *Harmful Algal Bloom ; RNA, Ribosomal, 16S ; }, abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.}, } @article {pmid40377844, year = {2025}, author = {Paul, B and Pan, P and Bhattacharyya, N}, title = {Investigating the impact of fly ash contamination on soil microbial diversity: a metagenomic study near Kolaghat Thermal Power Plant, India.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {23}, pages = {14002-14019}, pmid = {40377844}, issn = {1614-7499}, mesh = {India ; *Soil Microbiology ; *Coal Ash ; Metagenomics ; Power Plants ; *Soil Pollutants ; Bacteria ; Fungi ; Soil/chemistry ; Microbiota ; }, abstract = {Soil metagenomics using whole genome shotgun sequencing (WGS) uncovers microbial diversity and functionality in soils. This study aimed to explore microbial diversity and functional adaptation in soils exposed to fly ash near the Kolaghat Thermal Power Plant, West Bengal, India, using whole genome shotgun sequencing. Understanding how microbial communities respond to such contamination is essential for developing effective bioremediation strategies. Soil samples were collected from the area, designated as BP1 sample selected for detailed metagenomics analysis. The study extracted DNA with a concentration of 46.2 ng/µl, followed by quality checks and profiling to identify microbial communities. Analysis showed that bacterial communities were dominated by Actinobacteria (48.28%) and Proteobacteria (40.80%), while fungi were primarily represented by Ascomycota (89.50%). Among viruses, Negarnaviricota were most prevalent, with the class Insthoviricetes accounting for 94.60%. Diversity analysis indicated that bacterial populations remained stable, fungal diversity fluctuated, and viral diversity increased, reflecting complex ecological interactions. The presence of key genes involved in lipid and carbohydrate metabolism suggests that microbes adapted to contamination by heavy metals and organic pollutants. The dominance of stress-tolerant Proteobacteria and Actinobacteria highlights their potential role in bioremediation. Future research should explore the potential of these microbes, particularly the role of ABC transporters, in improving pollutant degradation.}, } @article {pmid40377187, year = {2025}, author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM}, title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {40377187}, issn = {2050-084X}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; 1746045//National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; }, abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.}, } @article {pmid40376801, year = {2025}, author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW}, title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.}, journal = {Circulation. Heart failure}, volume = {18}, number = {7}, pages = {e012524}, pmid = {40376801}, issn = {1941-3297}, support = {K08 HL168166/HL/NHLBI NIH HHS/United States ; R01 HL158795/HL/NHLBI NIH HHS/United States ; R01 HL162927/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Ventricular Dysfunction, Right/physiopathology/microbiology/etiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Rats ; *Pulmonary Arterial Hypertension/microbiology/physiopathology/therapy ; Humans ; Disease Models, Animal ; *Lacticaseibacillus rhamnosus ; *Ventricular Function, Right ; *Inflammation/microbiology ; Rats, Sprague-Dawley ; Middle Aged ; Female ; *Probiotics ; }, abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.

METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4×10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.

RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.

CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.}, } @article {pmid40373900, year = {2025}, author = {Yin, CY and Sadiq, H and Liao, WH and Wang, HN and Fu, Z and Yu, WG and Han, F}, title = {Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.}, journal = {International journal of biological macromolecules}, volume = {313}, number = {}, pages = {144153}, doi = {10.1016/j.ijbiomac.2025.144153}, pmid = {40373900}, issn = {1879-0003}, mesh = {*Polysaccharide-Lyases/chemistry/metabolism/genetics ; Humans ; *Gastrointestinal Microbiome ; Hyaluronic Acid/metabolism ; Substrate Specificity ; Enzyme Stability ; Hydrogen-Ion Concentration ; Temperature ; Amino Acid Sequence ; }, abstract = {Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.}, } @article {pmid40373419, year = {2025}, author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS}, title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.}, journal = {Meat science}, volume = {226}, number = {}, pages = {109848}, doi = {10.1016/j.meatsci.2025.109848}, pmid = {40373419}, issn = {1873-4138}, mesh = {*Meat Products/microbiology/analysis ; *Food Microbiology ; *Sodium Chloride/analysis ; *Food Handling/methods ; Animals ; Metagenomics ; Microbiota ; Bacteria ; Food Preservation/methods ; }, abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.}, } @article {pmid40373385, year = {2025}, author = {Xu, Z and Pei, Y and Wang, H and Li, X}, title = {Comparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {55}, number = {}, pages = {101530}, doi = {10.1016/j.cbd.2025.101530}, pmid = {40373385}, issn = {1878-0407}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Larva/microbiology/metabolism ; *Ranidae/microbiology/metabolism ; *Bufonidae/microbiology/metabolism ; }, abstract = {Bile acids (BAs) are cholesterol derivatives synthesized by the liver, exhibit variation between different species. Researchers have long appreciated that microbiota play the roles in the biotransformation of BAs. However, relatively few studies have been reported on microbial-mediated production and transformation of BAs in amphibians. Our focus here is principally on difference of intestinal microbial diversity and BAs profiles between two common amphibians, Bufo gargarizans (B. gargarizans) and Rana chensinensis (R. chensinensis) tadpoles, through intestinal targeted BAs metabolomics and fecal metagenomic sequencing. The results demonstrated that B. gargarizans possessed higher levels of total BAs and higher ratio of unconjugated / conjugated BAs. In addition, the relative abundance of microbiota with bile salt hydrolase (BSH) activity in B. gargarizans was significantly higher than that of R. chensinensis, which may facilitate the conversion of conjugated to unconjugated BAs. Meanwhile the higher prevalence of bile-acid-induced (BAI) gene encoding microbiota in R. chensinensis may promote the synthesis of deoxycholic acid (DCA). Furthermore, discrepancies in virulence factors (VFs) and energy metabolism were observed between the two species, which may be linked to differences in the microbiota. This study revealed substantial differences in intestinal microbes and BAs across amphibian species, emphasizing the significant impact of intestinal microbes on BAs metabolism.}, } @article {pmid40372916, year = {2025}, author = {Ramar, M and Wiscovitch-Russo, R and Yano, N and Singh, H and Lamere, E and Short, M and Gonzalez-Juarbe, N and Fedulov, AV}, title = {Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.}, journal = {Cell reports}, volume = {44}, number = {5}, pages = {115684}, pmid = {40372916}, issn = {2211-1247}, support = {R01 ES030227/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *DNA Methylation ; *Dendritic Cells/metabolism/immunology ; *Asthma/microbiology/immunology/genetics/pathology ; Mice ; Female ; Mice, Inbred C57BL ; *Bacteria ; Epigenesis, Genetic ; *Particulate Matter ; }, abstract = {Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.}, } @article {pmid40372371, year = {2025}, author = {Li, X and He, N and Wang, H and Wu, Z and Wang, M and Liang, H and Xiao, L and Yang, Z and Li, C and Xu, P and Dai, T and Li, S and Zou, Y}, title = {Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.}, journal = {Journal of applied microbiology}, volume = {136}, number = {5}, pages = {}, doi = {10.1093/jambio/lxaf119}, pmid = {40372371}, issn = {1365-2672}, support = {XMHT20220104017//Shenzhen Municipal Government of China/ ; }, mesh = {Animals ; *Colitis, Ulcerative/therapy/chemically induced/microbiology ; Mice ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Probiotics/administration & dosage/therapeutic use ; Cytokines/metabolism/blood ; Dextran Sulfate/adverse effects ; *Faecalibacterium/physiology/genetics ; Humans ; Disease Models, Animal ; Colon/microbiology ; Male ; Female ; Mice, Inbred C57BL ; }, abstract = {AIMS: This study explores the impact of Faecalibacterium longum CM04-06 on inflammatory bowel disease (IBD) by regulating gut microbiota in mice.

METHODS AND RESULTS: We reanalyzed the distribution of the CM04-06 genome in the metagenome of the IBD cohort and observed a significantly higher abundance of CM04-06 in healthy individuals compared to patients with UC or CD. The prophylactic administration of CM04-06 was evaluated for its effects on intestinal microbial diversity and community composition after a two-week trial in mice. The intestinal microbiota was characterized using metagenomic sequencing of fecal samples on the DNBSEQ platform. CM04-06 treatment resulted in a significant reduction in the Disease Activity Index (DAI) and histological scores, as well as a decrease in the levels of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α, in both the colon and serum of DSS-induced mice. Furthermore, supplementation with CM04-06 significantly reduced the levels of pro-inflammatory cytokines in both the colon and serum. Additionally, CM04-06 enhanced the integrity of the intestinal epithelial barrier by increasing the expression of tight junction proteins and mucin. Moreover, we observed greater abundances of Faecalibaculum rodentium, Alistipes onderdonkii, Alistipes shahii, and Bifidobacterium animalis after CM04-06 treatment.

CONCLUSIONS: CM04-06 prevents and alleviates intestinal inflammation by modulating the composition of the microbiota community, increasing the abundance of beneficial probiotics, and suppressing pro-inflammatory cytokine levels.}, } @article {pmid40372056, year = {2025}, author = {Kok, CR and Thissen, JB and Cerroni, M and Tribble, DR and Cancio, A and Tran, S and Schofield, C and Colombo, RE and Troth, T and Joya, C and Lalani, T and Be, NA}, title = {Field expedient stool collection methods for gut microbiome analysis in deployed military environments.}, journal = {mSphere}, volume = {10}, number = {6}, pages = {e0081824}, pmid = {40372056}, issn = {2379-5042}, support = {//Lawrence Livermore National Laboratory/ ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Specimen Handling/methods ; *Military Personnel ; Adult ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Young Adult ; Diarrhea/microbiology ; Middle Aged ; Travel ; }, abstract = {Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.}, } @article {pmid40371968, year = {2025}, author = {Jansen, D and Deleu, S and Caenepeel, C and Marcelis, T and Simsek, C and Falony, G and Machiels, K and Sabino, J and Raes, J and Vermeire, S and Matthijnssens, J}, title = {Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2499575}, pmid = {40371968}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/virology/microbiology ; *Virome ; Male ; Female ; Feces/virology ; Adult ; Gastrointestinal Microbiome ; Middle Aged ; *Bacteriophages/genetics/isolation & purification/classification ; Young Adult ; }, abstract = {Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.}, } @article {pmid40369676, year = {2025}, author = {Zhang, Y and Liu, H and Jing, H}, title = {Community differences and potential function along the particle size spectrum of microbes in the twilight zone.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {121}, pmid = {40369676}, issn = {2049-2618}, support = {424QN341//the Hainan Provincial Natural Science Foundation of China/ ; JRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; 2023YFC2812804//the National Key R&D Program of China/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; }, mesh = {Particle Size ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seawater/microbiology/chemistry ; *Microbiota/genetics ; Metagenomics/methods ; Carbon/metabolism ; Metagenome ; }, abstract = {BACKGROUND: The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.

RESULTS: Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.

CONCLUSION: Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.}, } @article {pmid40368959, year = {2025}, author = {Song, XL and Wang, ZJ and Yin, XW and Sun, YL and Jang, DJ and Hong, SK}, title = {The impact of nitrogen deposition on nitrogen metabolism in ryegrass lawn with different soil nutrient levels.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16755}, pmid = {40368959}, issn = {2045-2322}, mesh = {*Nitrogen/metabolism ; *Lolium/metabolism ; *Soil/chemistry ; Soil Microbiology ; Nitrogen Fixation ; Nitrification ; *Nutrients/metabolism ; Denitrification ; Nitrogen Cycle ; Microbiota ; Nitrates/metabolism ; }, abstract = {Nitrogen deposition is a crucial factor in global change, which is widespread across various regions globally. It has drawn extensive attention due to its direct modification of soil nitrogen retention and nitrogen species distribution, thereby influencing nitrogen metabolism across entire ecosystems. Previous studies on its influence on nitrogen metabolism have not reached a consensus. In an urban ryegrass lawn mesocosm experiment, we set two levels of nitrogen deposition and soil nutrients respectively, aiming to study the impacts of these factors on the N-cycling process through metagenomic analysis. The results demonstrated nitrogen deposition increased nitrification, nitrogen fixation, denitrification, and dissimilatory nitrate reduction, but decreased assimilatory nitrate reduction in the nitrogen metabolism process by changing soil nitrogen availability and the abundance of N-cycling functional genes in the soil microbial community. The soil nutrient levels exhibited effects opposite to those of nitrogen deposition, negatively impacting nitrification, denitrification, and nitrogen fixation in the nitrogen metabolism process. This work further elucidates the impacts of nitrogen deposition on the ecological functions of the ryegrass lawn with different soil nutrient levels, and predicts the potential impacts of intensified nitrogen deposition on these ecological functions. It provides valuable theoretical support for understanding and evaluating complex ecological interactions.}, } @article {pmid40368948, year = {2025}, author = {Serivichyaswat, PT and Scholte, T and Wilms, T and Stranddorf, L and van der Valk, T}, title = {Metagenomic biodiversity assessment within an offshore wind farm.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16786}, pmid = {40368948}, issn = {2045-2322}, mesh = {*Biodiversity ; *Metagenomics/methods ; North Sea ; Animals ; *Wind ; Seawater ; *DNA, Environmental/genetics/analysis ; Ecosystem ; *Metagenome ; Denmark ; }, abstract = {Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.}, } @article {pmid40367945, year = {2025}, author = {Antonaru, LA and Rad-Menéndez, C and Mbedi, S and Sparmann, S and Pope, M and Oliver, T and Wu, S and Green, DH and Gugger, M and Nürnberg, DJ}, title = {Evolution of far-red light photoacclimation in cyanobacteria.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {2539-2553.e4}, doi = {10.1016/j.cub.2025.04.038}, pmid = {40367945}, issn = {1879-0445}, mesh = {*Cyanobacteria/genetics/physiology/radiation effects ; *Light ; *Photosynthesis/genetics ; Phylogeny ; *Biological Evolution ; Multigene Family ; *Acclimatization ; Red Light ; }, abstract = {Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.}, } @article {pmid40367885, year = {2025}, author = {Mo, S and Wu, X and Kashif, M and Zeng, S and Sang, Y and Meng, C and He, S and Jiang, C}, title = {Effects of Spartina alterniflora invasion on carbon fixation and sulfate reduction in a subtropical marine mangrove ecosystem.}, journal = {Marine pollution bulletin}, volume = {217}, number = {}, pages = {118128}, doi = {10.1016/j.marpolbul.2025.118128}, pmid = {40367885}, issn = {1879-3363}, mesh = {*Wetlands ; *Carbon Cycle ; *Sulfates/metabolism ; *Introduced Species ; *Poaceae/physiology ; Geologic Sediments/microbiology ; Ecosystem ; *Rhizophoraceae ; }, abstract = {Mangrove sediments host diverse microbial communities that are crucial for carbon fixation, but their functions and pathways in subtropical ecosystems-particularly under Spartina alterniflora invasion and across varying sediment depths-remain unclear. This study employed metagenomic and qPCR analyses to explore microbial carbon fixation in Rhizophora stylosa, S. alterniflora, and bare beach habitats. Environmental factors like Cd, sulfide, pH, and salinity significantly influenced carbon fixation and sulfate reduction. Specifically, the invasion increased the abundance of key carbon fixation genes, including aclA/B, cbbL, and korA, which are involved in the Calvin-Benson-Bassham (CBB) and Arnon-Buchanan (rTCA) cycles, respectively. This shift in gene abundance was accompanied by elevated Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity (0.47-21.82 nmol CO2 g[-1] soil min[-1]), suggesting a potential increase in microbial CO2 fixation rates in S. alterniflora-invaded sediments. Sediment depth also affected the distribution of carbon fixation genes and carbon-metabolizing microbes. Desulfobacterota were identified as major contributors to carbon fixation via both the rTCA and CBB cycles. Moreover, a strong correlation was observed between carbon fixation and sulfate reduction. These findings reveal how S. alterniflora invasion impacts carbon fixation and enhance our understanding of the mangrove ecosystems' role in climate change regulation.}, } @article {pmid40367854, year = {2025}, author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL}, title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.}, journal = {The Science of the total environment}, volume = {982}, number = {}, pages = {179554}, doi = {10.1016/j.scitotenv.2025.179554}, pmid = {40367854}, issn = {1879-1026}, mesh = {*Glycine max/microbiology/physiology/growth & development ; *Rhizosphere ; *Floods ; *Microbiota ; Plant Roots/microbiology ; Seeds ; *Soil Microbiology ; }, abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.}, } @article {pmid40366862, year = {2025}, author = {Wang, L and Chen, X and Pollock, NR and Villafuerte Gálvez, JA and Alonso, CD and Wang, D and Daugherty, K and Xu, H and Yao, J and Chen, Y and Kelly, CP and Cao, Y}, title = {Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2505269}, pmid = {40366862}, issn = {1949-0984}, support = {R01 AI116596/AI/NIAID NIH HHS/United States ; T32 DK007760/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology ; *Clostridium Infections/microbiology ; Feces/microbiology ; Female ; Male ; *Clostridioides difficile/genetics/physiology ; Metagenomics ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Carrier State/microbiology ; Aged, 80 and over ; }, abstract = {Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.}, } @article {pmid40366770, year = {2025}, author = {Baba, Y and Tsuge, D and Aoki, R}, title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: a randomized, double-blind, placebo-controlled crossover trial.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {89}, number = {8}, pages = {1191-1202}, doi = {10.1093/bbb/zbaf071}, pmid = {40366770}, issn = {1347-6947}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Fatty Acids, Volatile/biosynthesis ; *Prebiotics/administration & dosage ; Double-Blind Method ; Cross-Over Studies ; Male ; Adult ; *Probiotics/administration & dosage/pharmacology ; *Carbohydrate Metabolism/drug effects ; Female ; Feces/microbiology/chemistry ; Inulin/administration & dosage/pharmacology ; Young Adult ; Middle Aged ; }, abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL + IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL + IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL + IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL + IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.}, } @article {pmid40366158, year = {2025}, author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB}, title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0174924}, pmid = {40366158}, issn = {2379-5077}, mesh = {*Soil Microbiology ; Forests ; *Fires ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Soil/chemistry ; *Tracheophyta ; *Viruses/genetics/classification/isolation & purification ; Microbiota ; Metagenome ; Virome ; }, abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.

IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.}, } @article {pmid40366141, year = {2025}, author = {Li, J and Zheng, K and Ding, W and Lu, L and Liang, Y and Xiong, Y and Wei, Z and Gao, C and Su, Y and Wang, Z and Chen, X and Bao, Z and Hu, X and McMinn, A and Wang, M}, title = {Healthy and moribund Zhikong scallops (Chlamys farreri) developed different viral communities during a mass mortality event.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0034225}, pmid = {40366141}, issn = {2379-5077}, support = {42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306156//National Natural Science Foundation of China/ ; LSKJ202203201//Ocean University of China/ ; ZR2024QD056//Department of Science and Technology of Shandong Province/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Pectinidae/virology ; *Virome/genetics ; Phylogeny ; Metagenome ; *Viruses/genetics/classification ; Metagenomics ; }, abstract = {UNLABELLED: Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves.

IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.}, } @article {pmid40366139, year = {2025}, author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ}, title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.}, journal = {mSphere}, volume = {10}, number = {6}, pages = {e0013725}, pmid = {40366139}, issn = {2379-5042}, support = {Center for Ethnic Studies research grant//The Ohio State University/ ; R21 AI174000/AI/NIAID NIH HHS/United States ; NIAIDR21AI174000/NH/NIH HHS/United States ; Science Diversity Leadership Award//Chan Zuckerberg Initiative (CZI)/ ; T32 Interdisciplinary Program in Microbe-Host Biology//The Ohio State University/ ; Advancing Research in Infection and Immunity//The Ohio State University/ ; }, mesh = {Humans ; *Anemia, Sickle Cell/microbiology ; *Microbiota ; Child ; Male ; Female ; *Mouth/microbiology ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Adolescent ; Child, Preschool ; Metagenomics ; *Nose/microbiology ; }, abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.

IMPORTANCE: The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.}, } @article {pmid40366134, year = {2025}, author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X}, title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0037525}, pmid = {40366134}, issn = {2379-5077}, support = {SCW1039//U.S. Department of Energy/ ; 1939//Joint Genome Institute/ ; 50220//Facilities Integrating collaborations for User Science/ ; }, mesh = {*Diatoms/growth & development/microbiology ; *Microbiota ; *Eutrophication ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Flavobacteriaceae/genetics/metabolism ; Metagenomics ; }, abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.}, } @article {pmid40365061, year = {2025}, author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L}, title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1571684}, pmid = {40365061}, issn = {1664-302X}, abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.

METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.

RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000×) and T3 (500×), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal α-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.

DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.}, } @article {pmid40363788, year = {2025}, author = {Zhou, L and Li, J and Ding, C and Zhou, Y and Xiao, Z}, title = {Mechanistic Advances in Hypoglycemic Effects of Natural Polysaccharides: Multi-Target Regulation of Glycometabolism and Gut Microbiota Crosstalk.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {9}, pages = {}, pmid = {40363788}, issn = {1420-3049}, support = {2024JJ8163//Hunan Natural Science Foundation/ ; C2023005//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 201923//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 2022ZYYGN06//2022 Annual Natural Drug Resources and Function Development Fund Project/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; Animals ; *Hypoglycemic Agents/pharmacology/chemistry/therapeutic use ; Signal Transduction/drug effects ; Insulin Resistance ; Glucose/metabolism ; }, abstract = {Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure-activity relationships, integration of the gut microbiota-metabolism-immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure-activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications.}, } @article {pmid40362493, year = {2025}, author = {Žukienė, G and Narutytė, R and Rudaitis, V}, title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.}, journal = {International journal of molecular sciences}, volume = {26}, number = {9}, pages = {}, pmid = {40362493}, issn = {1422-0067}, mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.}, } @article {pmid40362462, year = {2025}, author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R}, title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.}, journal = {International journal of molecular sciences}, volume = {26}, number = {9}, pages = {}, pmid = {40362462}, issn = {1422-0067}, support = {xxxxx//AFRRI/ ; }, mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; }, abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.}, } @article {pmid40361215, year = {2025}, author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q}, title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {537}, pmid = {40361215}, issn = {1479-5876}, support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; }, mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.

METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.

RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.

CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.}, } @article {pmid40360994, year = {2025}, author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W}, title = {The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {475}, pmid = {40360994}, issn = {1471-2164}, support = {31900327//National Natural Science Foundation of China/ ; 2023NSFSC1153//Natural Science Foundation of Sichuan Province of China/ ; }, mesh = {Animals ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Caudata/physiology/genetics/microbiology ; Heat-Shock Response ; Transcriptome ; Gene Expression Profiling ; Energy Metabolism ; Larva ; }, abstract = {The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.}, } @article {pmid40360555, year = {2025}, author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S}, title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {78}, pmid = {40360555}, issn = {2055-5008}, support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; }, abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.}, } @article {pmid40358997, year = {2025}, author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R}, title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e64894}, pmid = {40358997}, issn = {1929-0748}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; }, abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.}, } @article {pmid40358144, year = {2025}, author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW}, title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.}, journal = {mSphere}, volume = {10}, number = {6}, pages = {e0091324}, pmid = {40358144}, issn = {2379-5042}, support = {R01 DK121689/DK/NIDDK NIH HHS/United States ; }, mesh = {*Oxalates/metabolism ; *Phylogeny ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Selection, Genetic ; }, abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.}, } @article {pmid40356191, year = {2025}, author = {Charalambous, H and Brown, C and Vogazianos, P and Katsaounou, K and Nikolaou, E and Stylianou, I and Papageorgiou, E and Vraxnos, D and Aristodimou, A and Chi, J and Costeas, P and Shammas, C and Apidianakis, Y and Antoniades, A}, title = {Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.}, journal = {Thoracic cancer}, volume = {16}, number = {9}, pages = {e70075}, pmid = {40356191}, issn = {1759-7714}, support = {//Investigator-Initiated Studies Program of Merck Sharp & Dohme Corp/ ; }, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects ; *Antineoplastic Agents, Immunological/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology ; Case-Control Studies ; *Dysbiosis/chemically induced/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Lung Neoplasms/drug therapy/pathology/microbiology ; Prospective Studies ; Pilot Projects ; }, abstract = {BACKGROUND: The gut microbiome influences the host immune system, cancer development and progression, as well as the response to immunotherapy during cancer treatment. Here, we analyse the composition of the gut bacteriome in metastatic Non-Small Cell Lung Cancer (NSCLC) patients receiving Pembrolizumab immunotherapy within a prospective maintenance trial through opportunistic sampling during treatment.

METHODS: The gut microbiome profiles of NSCLC patients were obtained from stool samples collected during Pembrolizumab treatment and analysed with 16S rRNA metagenomics sequencing. Patient profiles were compared to a group of healthy individuals of matching ethnic group, age, sex, BMI and comorbidities.

RESULTS: A significant decrease in the treated patients was observed in two prominent bacterial families of the phylum Firmicutes, Lachnospiraceae and Ruminoccocaceae, which comprised 31.6% and 21.8% of the bacteriome in the healthy group but only 10.9% and 14.2% in the treated patient group, respectively. Species within the Lachnospiraceae and Ruminococcaceae families are known to break down undigested carbohydrates generating short chain fatty acids (SCFA), such as butyrate, acetate and propionate as their major fermentation end-products, which have been implicated in modifying host immune responses. In addition, a significant increase of the Bacteroidacaeae family (Bacteroidetes phylum) was observed from 10.7% in the healthy group to 23.3% in the treated patient group. Moreover, and in agreement with previous studies, a decrease in the Firmicutes to Bacteroidetes ratio in the metastatic NSCLC Pembrolizumab-treated patients was observed.

CONCLUSION: The observed differences indicate dysbiosis and a compromised intestinal health status in the metastatic NSCLC Pembrolizumab-treated patients. This data could inform future studies of immunotherapy treatment responses and modulation of the gut microbiome to minimise dysbiosis prior or concurrent to treatment.

TRIAL REGISTRATION: SWIPE Trial (NCT02705820).}, } @article {pmid40356165, year = {2025}, author = {Park, C and Park, J and Chang, D and Kim, S}, title = {Development of reference-based model for improved analysis of bacterial community.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116380}, doi = {10.1016/j.foodres.2025.116380}, pmid = {40356165}, issn = {1873-7145}, mesh = {RNA, Ribosomal, 16S/genetics ; *Probiotics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; }, abstract = {Probiotic bacteria play a vital role in maintaining gut microbial homeostasis and are widely used in various commercial products. Although 16S rRNA amplicon-based next-generation sequencing (NGS) is commonly used to analyze probiotic products, biases can arise from various 16S rRNA amplification regions, sequencing platforms, and library kits. In this study, a reference-based bias correction model was developed to correct sequencing biases. The model was validated using eight mock communities and 12 commercial products, which were analyzed across multiple NGS platforms and various 16S rRNA regions. Specific primer-probe assays were developed for accurate bacterial quantification, and their specificity was validated and used in conjunction with droplet digital PCR (ddPCR) to establish initial bacterial ratios within communities. Analysis of the mock communities revealed platform- and region-specific biases, with specific species consistently over- or under-represented. Similarly, commercial product analyses have shown biased outcomes owing to varying sequencing protocols. The correction model, based on PCR efficiencies from the reference communities, successfully corrected biased ratios across different amplification regions and platforms to achieve results that closely matched the proportions predicted by ddPCR. The model effectively corrected the biases arising from the different polymerases. Notably, partial references containing approximately 40 % of the species achieved correction results that were comparable to those of the complete references. This approach demonstrates the potential for improving microbiome analysis accuracy within predictable ranges, and could serve as a model for addressing sequencing bias in metagenomic research.}, } @article {pmid40356145, year = {2025}, author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q}, title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116488}, doi = {10.1016/j.foodres.2025.116488}, pmid = {40356145}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; }, abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.}, } @article {pmid40356136, year = {2025}, author = {Luo, Y and Tang, R and Huang, Y}, title = {Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116474}, doi = {10.1016/j.foodres.2025.116474}, pmid = {40356136}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Rubus/chemistry ; *Antioxidants/pharmacology/chemistry ; *Pectins/chemistry/pharmacology ; Prebiotics/analysis ; *Polysaccharides/chemistry/pharmacology ; *Fruit/chemistry ; Humans ; *Plant Extracts/chemistry/pharmacology ; }, abstract = {Red raspberries are associated with various health benefits, with pectic polysaccharides as their primary component and potential key contributor to these effects. This study aimed to evaluate the antioxidant and prebiotic potential of four red raspberry pectic polysaccharides (RP)-EN-RP (enzyme-assisted extraction), AC-RP (acid-assisted extraction), AL-RP (alkali-assisted extraction), and US-RP (ultrasound-assisted extraction)-and to elucidate the relationship between their structure and function. AC-RP and US-RP contained higher proportions of homogalacturonan (HG) at 50.92 % and 53.10 %, respectively, while EN-RP and AL-RP exhibited higher proportions of rhamnogalacturonan-I (RG-I) at 63.89 % and 43.37 %, respectively. All four polysaccharides demonstrated significant antioxidant and prebiotic properties. AL-RP exhibited the strongest DPPH radical scavenging activity, while US-RP showed the highest hydroxyl radical scavenging ability. These pectic polysaccharides were highly fermentable, significantly modulating gut microbiota composition and promoting the production of propionic acid, particularly EN-RP and AL-RP. Compared to the blank group, RP intervention significantly enriched Bacteroides, Phocaeicola, Bifidobacterium, Limosilactobacillus, and Paraprevotella. Carbohydrate-active enzyme genes in metagenomes revealed that glycoside hydrolases played a vital role in the degradation and utilization of red raspberry polysaccharides. Furthermore, correlation analysis indicated that a higher RG-I proportion and an elevated Rha/GalA ratio enhanced the abundance of certain beneficial microbial species and increased propionic acid production. These findings advance the understanding of the structure-function relationship of natural pectic polysaccharides and highlight their potential for tailoring gut microbiota and promoting health through precise dietary interventions.}, } @article {pmid40355758, year = {2025}, author = {Saeedi Saravi, SS and Pugin, B and Constancias, F and Shabanian, K and Spalinger, M and Thomas, A and Le Gludic, S and Shabanian, T and Karsai, G and Colucci, M and Menni, C and Attaye, I and Zhang, X and Allemann, MS and Lee, P and Visconti, A and Falchi, M and Alimonti, A and Ruschitzka, F and Paneni, F and Beer, JH}, title = {Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging.}, journal = {Nature aging}, volume = {5}, number = {6}, pages = {1025-1045}, pmid = {40355758}, issn = {2662-8465}, support = {/WT_/Wellcome Trust/United Kingdom ; #21A053//Novartis Stiftung für Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; #310030_21A053//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #CRSK-3_229134//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Phenylacetates/metabolism/blood ; *Cellular Senescence/physiology/drug effects ; *Aging/metabolism ; Humans ; Mice ; *Endothelial Cells/metabolism ; Male ; Clostridium/metabolism ; Mice, Inbred C57BL ; Hydrogen Peroxide/metabolism ; Female ; Glutamine/analogs & derivatives/metabolism ; Feces/microbiology/chemistry ; Aged ; Mitochondria/metabolism ; Sirtuin 1/metabolism ; }, abstract = {Endothelial cell senescence is a key driver of cardiovascular aging, yet little is known about the mechanisms by which it is induced in vivo. Here we show that the gut bacterial metabolite phenylacetic acid (PAA) and its byproduct, phenylacetylglutamine (PAGln), are elevated in aged humans and mice. Metagenomic analyses reveal an age-related increase in PAA-producing microbial pathways, positively linked to the bacterium Clostridium sp. ASF356 (Clos). We demonstrate that colonization of young mice with Clos increases blood PAA levels and induces endothelial senescence and angiogenic incompetence. Mechanistically, we find that PAA triggers senescence through mitochondrial H2O2 production, exacerbating the senescence-associated secretory phenotype. By contrast, we demonstrate that fecal acetate levels are reduced with age, compromising its function as a Sirt1-dependent senomorphic, regulating proinflammatory secretion and redox homeostasis. These findings define PAA as a mediator of gut-vascular crosstalk in aging and identify sodium acetate as a potential microbiome-based senotherapy to promote healthy aging.}, } @article {pmid40355744, year = {2025}, author = {Schreiber, S and Waetzig, GH and López-Agudelo, VA and Geisler, C and Schlicht, K and Franzenburg, S and di Giuseppe, R and Pape, D and Bahmer, T and Krawczak, M and Kokott, E and Penninger, JM and Harzer, O and Kramer, J and von Schrenck, T and Sommer, F and Zacharias, HU and , and Millet Pascual-Leone, B and Forslund, SK and Heyckendorf, J and Aden, K and Hollweck, R and Laudes, M and Rosenstiel, P}, title = {Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.}, journal = {Nature metabolism}, volume = {7}, number = {6}, pages = {1136-1149}, pmid = {40355744}, issn = {2522-5812}, support = {EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: RTF-VI//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SO1141/10-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1470, SFB1449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-2, RTF-VI, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med CKDNapp 01ZX1912A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; K126408//Christian-Albrechts-Universität zu Kiel (Christian-Albrechts-University Kiel)/ ; }, mesh = {Humans ; *Niacinamide/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Double-Blind Method ; *COVID-19/metabolism ; Female ; Middle Aged ; SARS-CoV-2 ; *COVID-19 Drug Treatment ; Adult ; Feces/microbiology ; Prospective Studies ; Aged ; Dysbiosis ; Tryptophan/metabolism ; }, abstract = {Cellular NAD[+] depletion, altered tryptophan metabolism and gut microbiome dysbiosis are associated with disease progression and unfavourable clinical outcomes in COVID-19. Here, we show that supplementing tryptophan metabolism with nicotinamide alleviates COVID-19 symptoms. We evaluate a 4-week intervention with a novel nicotinamide formulation (1,000 mg) in a prospective, double-blind, randomized, placebo-controlled trial in 900 symptomatic outpatients with PCR-proven COVID-19. In the primary analysis population of participants at risk for severe COVID-19, 57.6% of those receiving nicotinamide and 42.6% receiving placebo recover from their performance drop at week 2 (P = 0.004). Nicotinamide is also beneficial for returning to normal activities (P = 0.009). Effects on gut metagenomic signatures parallel clinical efficacy, suggesting that nicotinamide influences COVID-19-associated faecal microbiome changes. After 6 months, responders to nicotinamide in acute COVID-19 show fewer post-COVID symptoms than placebo responders (P = 0.010). No relevant safety signals are observed. Overall, our results show that nicotinamide leads to faster recovery of physical performance and modulates COVID-19-associated faecal microbiome changes.}, } @article {pmid40355385, year = {2025}, author = {Wang, L and Chen, Y and Wang, Q and Wang, F}, title = {Microbial imbalances linked to early pregnancy loss: a comparative analysis of vaginal microbiota.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {38}, number = {1}, pages = {2496787}, doi = {10.1080/14767058.2025.2496787}, pmid = {40355385}, issn = {1476-4954}, mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Case-Control Studies ; *Abortion, Spontaneous/microbiology ; Adult ; *Microbiota ; Young Adult ; }, abstract = {OBJECTIVE: To explore the role and related functions of vaginal microbiota in early pregnancy loss.

METHODS: This study was a case-control study with a comparison group (reference group). We recruited 178 women, including 73 who had experienced at least one early clinical pregnancy loss and 105 patients with one live birth and no history of pregnancy loss. Data on demographics, disease history, menstrual and reproductive history was collected. The case group patients were sampled immediately upon presenting with pregnancy loss at their first visit. The reference group patients underwent samples when they chose to participate voluntarily. All vaginal discharge was performed DNA Preparation and Metagenomics Sequencing. DNA extraction was performed using the phenol/trichloromethane method and the DNA fragments were then size-selected to 300-700 bp using magnetic beads. The selected fragments were repaired and ligated with indexed adaptors. The captured DNA was amplified again by PCR and circularized to create a single-stranded circular (ssCir) library. The ssCir library was subsequently amplified through rolling circle amplification (RCA) to produce DNA nanoballs (DNBs). The DNBs were then loaded onto a flow cell and sequenced using the DNBSEQ Platform. Nonparametric tests, including Kruskal-Wallis and Wilcoxon tests, were employed. Relative abundance between groups was compared, and differential species selection was performed using the LEfSe software with linear discriminant analysis.

RESULTS: 1. PCoA analysis based on Bray-Curtis distances at the species level revealed a difference between the groups (p = 0.011). At the genus level, α-diversity, assessed using the Shannon, Simpson, and Inverse Simpson indices, indicated higher bacterial richness and diversity in the control group (Shannon: mean 0.554 vs. 0.383, p = 0.0044; Simpson: mean 0.254 vs. 0.179, p = 0.0043; Inverse Simpson: mean 1.636 vs. 1.414, p = 0.0043); At the genus level, 107 microbial genera were identified, 18 of which displayed statistically significant differences. At the species level, 23 microbial species showed significant differences between the two groups. 2. We analyzed the differences in the most abundant phyla, genera, and species, with a particular focus on the top 20 most abundant genera and species. Firmicutes and Proteobacteria were significantly more prevalent among patients with pregnancy loss (PL). Among the top 20 most abundant genera, Streptococcus and Porphyromonas were significantly more abundant in patients with PL, whereas Bifidobacterium was significantly more prevalent in the reference group. Among the 20 most abundant species, Lactobacillus crispatus was significantly more prevalent in patients with PL, whereas common in the control group. 3. Principal Coordinates Analysis (PCoA) of Bray-Curtis distances, highlight their distinct clustering patterns, suggesting a notable difference between the metabolic pathways of the two groups. Key pathways with a negative correlation to PL include those related to amino acid biosynthesis, lipid metabolism, and nucleotide biosynthesis.

CONCLUSION: Our study highlights the association between vaginal microbiota dysbiosis and EPL, identifying specific microbial taxa that may contribute to pregnancy loss. These findings underscore the importance of the vaginal microbiome in reproductive health and open up new avenues for research into microbiome-based diagnostics and therapies. By integrating microbial, immune, and environmental data, future research has the potential to uncover the mechanisms underlying EPL and develop targeted interventions to improve pregnancy outcomes.}, } @article {pmid40354675, year = {2025}, author = {Zhi, N and Chang, X and Zha, L and Zhang, K and Wang, J and Gui, S}, title = {Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {142}, number = {}, pages = {156653}, doi = {10.1016/j.phymed.2025.156653}, pmid = {40354675}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; *Obesity/drug therapy/metabolism ; *Platycodon/chemistry ; Diet, High-Fat/adverse effects ; Mice ; Fatty Acids, Volatile/metabolism ; *Anti-Obesity Agents/pharmacology ; Drugs, Chinese Herbal ; }, abstract = {BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.

PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.

STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.

RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.

CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.}, } @article {pmid40350519, year = {2025}, author = {Schultz, J and Jamil, T and Sengupta, P and Sivabalan, SKM and Rawat, A and Patel, N and Krishnamurthi, S and Alam, I and Singh, NK and Raman, K and Rosado, AS and Venkateswaran, K}, title = {Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {117}, pmid = {40350519}, issn = {2049-2618}, support = {BAS/1/1096-01-01//KAUST Baseline Grant/ ; PPR-ROSES-2006//National Aeronautical and Space Administration/ ; }, mesh = {*Spacecraft ; United States National Aeronautics and Space Administration ; *Bacteria/genetics/isolation & purification/classification ; United States ; Biofilms/growth & development ; Space Flight ; *Extremophiles/genetics/isolation & purification/classification ; *Genome, Bacterial ; Humans ; Microbiota/genetics ; Genomics ; Metagenome ; Phylogeny ; }, abstract = {BACKGROUND: Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.

RESULTS: During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n = 13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for ε-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited for zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.

CONCLUSION: Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.}, } @article {pmid40350492, year = {2025}, author = {Ding, Y and Ke, J and Hong, T and Zhang, A and Wu, X and Jiang, X and Shao, S and Gong, M and Zhao, S and Shen, L and Chen, S}, title = {Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {287}, pmid = {40350492}, issn = {1471-2180}, support = {STEP 2024QZKK02010//Supported by the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2208085MC39//Natural Science Foundation of Anhui Province, China/ ; }, mesh = {China ; *Lakes/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Archaea/classification/genetics/isolation & purification ; Phylogeny ; DNA, Archaeal/genetics ; Salinity ; *Biodiversity ; Alkalies/analysis ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; Sodium Chloride ; Sequence Analysis, DNA ; Bacteria/classification/genetics ; }, abstract = {Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.}, } @article {pmid40350460, year = {2025}, author = {Zhang, X and Zhong, R and Wu, J and Tan, Z and Jiao, J}, title = {Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {118}, pmid = {40350460}, issn = {2049-2618}, support = {32372829, 31972992//National Natural Science Foundation of China/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; 2022RC1158//The Science and Technology innovation Program of Hunan Province/ ; 2023382//Youth Innovation Promotion Association CAS/ ; }, mesh = {Animals ; *Goats/microbiology ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; Animal Feed/analysis ; Metagenomics/methods ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fibrobacter/metabolism/genetics/isolation & purification ; Ruminococcus/metabolism/genetics/isolation & purification ; Diet/veterinary ; Cecum/microbiology/metabolism ; Cellulose/metabolism ; Fatty Acids, Volatile/metabolism ; Polysaccharides/metabolism ; *Gastrointestinal Tract/microbiology ; }, abstract = {BACKGROUND: Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.

RESULTS: The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).

CONCLUSIONS: These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.}, } @article {pmid40350266, year = {2025}, author = {Ohyama, Y and Miura, T and Furukawa, M and Shimamura, M and Asami, Y and Yamazoe, A and Uchino, Y and Kawasaki, H}, title = {A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.}, journal = {Microbes and environments}, volume = {40}, number = {2}, pages = {}, pmid = {40350266}, issn = {1347-4405}, mesh = {Chromatography, High Pressure Liquid/methods ; *Bacteria/genetics/isolation & purification/classification ; Humans ; *Microbiota/genetics ; *Genome, Bacterial ; Metagenomics/methods ; Reproducibility of Results ; }, abstract = {Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.}, } @article {pmid40350102, year = {2025}, author = {El-Son, MAM and Elbahnaswy, S and Khormi, MA and Aborasain, AM and Abdelhaffez, HH and Zahran, E}, title = {Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture.}, journal = {Fish & shellfish immunology}, volume = {163}, number = {}, pages = {110394}, doi = {10.1016/j.fsi.2025.110394}, pmid = {40350102}, issn = {1095-9947}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Aquaculture/methods ; *Fishes/immunology/microbiology ; *Disease Resistance/immunology ; Probiotics/administration & dosage ; *Fish Diseases/immunology/prevention & control/microbiology ; Prebiotics/administration & dosage ; Diet/veterinary ; }, abstract = {The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.}, } @article {pmid40349412, year = {2025}, author = {Ren, P and You, C and Chen, P and Mei, X and Yang, T and Xu, Y and Wang, X and Shen, Q and Wei, Z}, title = {Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128213}, doi = {10.1016/j.micres.2025.128213}, pmid = {40349412}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Fertilizers/analysis ; Bacteria/classification/genetics/isolation & purification ; China ; Biodiversity ; Lysobacter ; }, abstract = {Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.}, } @article {pmid40349120, year = {2025}, author = {Jiang, S and Huang, S and Zhang, Z and Ma, W and Han, Z and Song, Y and Huo, D and Cui, W and Zhang, J}, title = {Gut microbiota drives structural variation of exogenous probiotics to enhance colonization.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2503371}, pmid = {40349120}, issn = {1949-0984}, mesh = {*Probiotics/pharmacology ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Lactobacillus plantarum/genetics/growth & development ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts ; Metagenomics ; }, abstract = {Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.}, } @article {pmid40348945, year = {2025}, author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H}, title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {114}, number = {5}, pages = {77}, pmid = {40348945}, issn = {1432-0800}, support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; }, mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; }, abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.}, } @article {pmid40348632, year = {2025}, author = {Lotankar, M and Houttu, N and Benchraka, C and Lahti, L and Laitinen, K}, title = {Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {35}, number = {9}, pages = {104095}, doi = {10.1016/j.numecd.2025.104095}, pmid = {40348632}, issn = {1590-3729}, mesh = {Adult ; Female ; Humans ; Pregnancy ; Young Adult ; *Bacteria/metabolism/genetics/classification ; Biomarkers/blood ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Magnetic Resonance Spectroscopy ; *Metabolome ; *Metabolomics/methods ; Metagenomics ; *Obesity/diagnosis/microbiology/blood ; *Pregnancy Complications/blood/diagnosis/microbiology ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {BACKGROUND AND AIM: Gut microbiota may regulate metabolism but is incompletely characterized in pregnancy. Our objective was to investigate the relations using omics techniques.

METHODS AND RESULTS: In a cross-sectional setting, fecal and serum samples of 361 healthy pregnant women with overweight or obesity were analyzed with a combinatorial approach of metagenomics and targeted NMR-based metabolomics, with statistical and machine learning techniques to identify and analyze the extent to which the gut microbiota composition and predicted functions would be reflected in the serum metabolome. We identified five biclusters, each of which consisted of a set of gut microbial species and serum metabolites with correlated abundance profiles. Two of the biclusters included metabolites that have been linked to the cardiovascular health; one was linked with factors known to increase the risk i.e., various sizes of lipoprotein subclasses (VLDL and LDL), subclasses of relative lipoprotein lipid concentrations (VLDL, IDL, and LDL), apolipoprotein B, and an inflammation marker, glycoprotein acetylation. These metabolites were associated with abundances of species such as, Enterocloster bolteae and Ruminococcus gnavus. The second bicluster included metabolites linked with a reduced cardiovascular risk, such as different sizes of HDL (high-density lipoprotein), subclasses for relative lipoprotein lipid concentrations and mean diameter for HDL particles, and fatty acid ratios. These metabolites were associated with abundances of species, such as Bacteroides cellulosilyticus and Alistipes finegoldii. We did not observe any biclusters between predicted pathways and serum metabolites.

CONCLUSION: Overall, we identified five biclusters of co-abundant gut bacteria and serum metabolites , of which two were linked to pro-atherogenic and anti-atherogenic properties.

TRIAL REGISTRATION: www.

CLINICALTRIALS: Gov: NCT01922791.}, } @article {pmid40348492, year = {2025}, author = {Quigley, EMM}, title = {Microbial Influences on Irritable Bowel Syndrome.}, journal = {Gastroenterology clinics of North America}, volume = {54}, number = {2}, pages = {351-365}, doi = {10.1016/j.gtc.2024.12.003}, pmid = {40348492}, issn = {1558-1942}, mesh = {*Irritable Bowel Syndrome/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolomics ; Metagenomics ; Dysbiosis ; }, abstract = {Since the description of postinfection irritable bowel syndrome (IBS), a role for gut microbes in the pathogenesis of IBS has been proposed. Molecular microbiological tools have now been applied to IBS, though data are largely derived from fecal samples with attendant limitations. Metagenomics, metabolomics, and other 'omics facilitate a comprehensive picture of the microbiome and its metabolic activity. Has a microbial signature characteristic of IBS been identified? The answer is no; this should not be a surprise given the heterogeneity of the phenotype and each individual's microbiome profile.}, } @article {pmid40348210, year = {2025}, author = {Lin, Z and Zhang, P and Shi, D and Zhang, Y and Wu, W and Tang, Q and Wang, Q and Wang, S}, title = {Association between the gut microbiota and cystitis: A two-sample mendelian randomization study combined with the GEO database.}, journal = {Microbial pathogenesis}, volume = {205}, number = {}, pages = {107683}, doi = {10.1016/j.micpath.2025.107683}, pmid = {40348210}, issn = {1096-1208}, mesh = {*Cystitis/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; Metagenomics ; Dysbiosis/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: Disturbances within the intestinal microbiota have emerged as a significant factor contributing to systemic inflammation, thereby rendering distant anatomical sites more vulnerable to various illnesses, including inflammatory conditions in the urinary tract such as cystitis. However, the causal relationship between dysbiosis of the gut microbiota and cystitis remains unclear. We sought to elucidate the causal relationship between the intestinal microbiota and cystitis employing Mendelian randomization (MR), offering insights into novel preventive and therapeutic strategies for managing cystitis.

METHOD: Summary statistics for the Genome-Wide Association Study (GWAS) of cystitis were sourced from the R5 release dataset provided by the FinnGen consortium, which included 8081 cystitis cases and 195,140 controls. Single Nucleotide Polymorphisms (SNPs) that showed strong associations with 196 microbial taxa (encompassing 18,340 individuals) were selected as instrumental variables. To analyze the causal relationships between cystitis and gut microbiota, we employed four MR analysis methods: random effects, inverse variance weighting, weighted medians, and MR-Egger regression. Sensitivity analyses were performed using the Cochran's Q test, funnel plots, leave-one-out analyses, and the MR-Egger intercept test. We conducted metagenomic analysis of fecal samples from 7 patients with cystitis and 7 healthy controls to validate the findings from our MR results. To further elucidate the biological mechanisms, we conducted positional mapping of the extracted SNPs associated with the significant taxa. Additionally, we curated differentially expressed genes (DEGs) from three datasets about cystitis obtained from the Gene Expression Omnibus (GEO). Finally, we intersected the DEGs with the mapped genes to identify common genes of cystitis.

RESULTS: Our analysis revealed significant associations between specific gut microbiota and cystitis. IVW results revealed that four gut microorganisms, specifically, the genus RuminococcaceaeUCG011, genus Sutterella, family Porphyromonadaceae, and family Veillonellaceae (P < 0.05), contributed to a reduction in the incidence of cystitis. Similarly, four cystitis-related bacteria, namely, the genus Marvinbryantia, the genus Odoribacter, the genus Ruminiclostridium6, and the genus Sellimonas, are thought to play a significant role in elevating the risk of cystitis (P < 0.05). The metagenomic analysis revealed significant differences in the abundance of the genera Sutterella and Odoribacter in patients with cystitis compared to healthy controls. Additionally, we mapped causal SNPs to genes and identified 62 genes. Bioinformatics analysis reveals 161 common DEGs in cystitis. Through MR and bioinformatics analysis, we identified two common genes-ICAM1 and HP-as potential targets for cystitis.

CONCLUSION: Our research identified genetic connections between eight components of gut microbiota and two genes related to cystitis. These results offer important insights for subsequent studies into the complex relationship between gut microbiota and cystitis.}, } @article {pmid40347566, year = {2025}, author = {Jiang, J and Wu, H and Yuan, Y}, title = {Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca).}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {55}, number = {}, pages = {101529}, doi = {10.1016/j.cbd.2025.101529}, pmid = {40347566}, issn = {1878-0407}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Ursidae/microbiology/metabolism ; *Feces/microbiology/chemistry ; *Metabolome ; Animal Feed/analysis ; }, abstract = {The influences of different bamboo species on the microbiome and metabolome of giant pandas (Ailuropoda melanoleuca) remain understudied. The aim of this study was to investigate the effects of different Phyllostachys species on the gut microbial communities and fecal metabolite profiles in giant pandas. Metagenome and metabolome were performed on the feces of giant pandas fed with different Phyllostachys species (P. edulis, P. iridescens, P. glauca, and P. violascens). The results of metagenome showed that dietary with P. glauca could notably decrease the microbial Shannon index. The relative abundances of both Cellulosilyticum and Pseudomonas were enhanced after dietary with P. iridescens, suggesting P. iridescens could enhance the cellulose-degrading function in giant pandas. However, dietary with P. glauca or P. violascens could increase the relative abundances of certain pathogenic bacteria (Escherichia, Shigella, and Klebsiella). Metabolomics analysis further revealed that all experimental groups exhibited notably elevated levels of fecal flavonoids and fatty acids. In addition, the correlation analysis showed that certain nutrients of bamboo leaves (mainly crude protein and Cu) were significantly correlated with several differential gut bacteria and fecal metabolites. Based on the present results, P. iridescens might be a substitute for the routinely used Phyllostachys species (P. edulis) in the captive management of giant pandas. The results have revealed that bamboo species is an important factor affecting the gut microbiota and fecal metabolites in giant pandas. Our results could provide important information about bamboo species-induced alterations on the microbiome and metabolome in giant pandas.}, } @article {pmid40346812, year = {2025}, author = {Pryor, JC and Nieva, C and Talley, NJ and Eslick, GD and Duncanson, K and Burns, GL and Hoedt, EC and Keely, S}, title = {Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2500063}, pmid = {40346812}, issn = {1949-0984}, mesh = {Humans ; *Bacteria/enzymology/genetics/classification/isolation & purification ; *Celiac Disease/microbiology/enzymology ; *Duodenum/microbiology ; *Dyspepsia/microbiology ; *Gastrointestinal Microbiome ; *Glutens/metabolism ; *Peptide Hydrolases/metabolism/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.}, } @article {pmid40346542, year = {2025}, author = {Gao, H and Xu, L and Liu, Y and Wang, X and Zhu, S and Lin, H and Gao, Y and Mao, D and Lu, X and Luo, Y}, title = {Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.}, journal = {Respiratory research}, volume = {26}, number = {1}, pages = {178}, pmid = {40346542}, issn = {1465-993X}, support = {2022BKY015//the Tianjin Graduate Research and Innovation Projects/ ; 42377426//the National Natural Science Foundation of China/ ; 18ZXDBSY00100//the Tianjin Science and Technology Plan Project/ ; 21JCYBJC01200//the Tianjin Municipal Natural Science Foundation/ ; 2023220//the Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; 2020YFC1806904//the National Key R&D Program of China/ ; 41831287//the Key Projects of the National Natural Science Foundation of China/ ; }, mesh = {Aged ; Animals ; Female ; Humans ; Male ; Mice ; Middle Aged ; *Bacterial Translocation/physiology/genetics ; *Burkholderia cenocepacia/genetics/isolation & purification/pathogenicity ; *Escherichia coli/genetics/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; Intensive Care Units/trends ; *Lung/microbiology ; Mice, Inbred C57BL ; *Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics ; Whole Genome Sequencing/methods ; Case-Control Studies ; Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Identifying the sources of pathogenic bacteria causing ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients is crucial for developing effective prevention and treatment strategies. However, the scarcity of reported cases with confirmed sources limits the ability to evaluate and manage VAP, which remains a major challenge for healthcare systems globally.

METHODS: Pathogens were isolated from endotracheal aspirate (ETA) samples of VAP patients using conventional culture techniques. Whole-genome comparisons, based on average nucleotide identity (ANI), were performed to identify genetically identical strains by comparing pulmonary isolate genomes with gut metagenome-derived bacterial genomes. Mouse models of pneumonia and colitis were used to validate the translocation of pathogenic bacteria from the gut to the lungs. Metagenomic analysis was performed to characterize the gut microbiome and resistome.

RESULTS: Pathogenic isolates were obtained from the ETA samples of seven VAP patients, with one isolate per sample. Among these, Escherichia coli (Ec1) and Burkholderia cenocepacia (Bc1) from two patients were genetically identical to strains in their respective gut microbiota, with ANI values above 99%, indicating gut-to-lung translocation. The Ec1 strain demonstrated increased resistance to cefazolin while remaining susceptible to gentamicin, amikacin, and kanamycin, compared to previously reported pneumonia-associated E. coli strains. The Bc1 strain showed elevated resistance to macrolides, chloramphenicols, and tetracyclines relative to pneumonia-associated B. cenocepacia strains. Metagenomic analysis revealed a highly individualized gut microbiota composition among VAP patients. Notably, the translocated bacteria were not dominant within their gut microbiota. Additionally, these patients showed a marked increase in the total abundance of antibiotic resistance genes (ARGs) in their gut microbiota. The translocation ability of the Ec1 strain was validated in a mouse pneumonia model, where it caused more severe lung damage. Furthermore, elevated levels of Escherichia-Shigella were detected in the lung tissues of colitis mice, suggesting that gut-to-lung bacterial translocation may occur in a severely inflamed host, potentially leading to pneumonia.

CONCLUSIONS: This study demonstrates the gut-to-lung translocation of E. coli and B. cenocepacia, highlighting their role in the development and progression of VAP in ICU patients. These findings provide valuable insights for implementing targeted prevention and treatment strategies for VAP in ICU settings.}, } @article {pmid40344797, year = {2025}, author = {Chen, Y and Liu, Q and Xu, XW}, title = {Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions.}, journal = {Marine pollution bulletin}, volume = {217}, number = {}, pages = {118121}, doi = {10.1016/j.marpolbul.2025.118121}, pmid = {40344797}, issn = {1879-3363}, mesh = {*Estuaries ; Rivers/microbiology ; China ; *Nitrogen Cycle ; *Microbiota ; Nitrogen ; Seawater/microbiology ; Spatio-Temporal Analysis ; Bacteria/metabolism ; Environmental Monitoring ; Salinity ; Denitrification ; }, abstract = {Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3[-]]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.}, } @article {pmid40344252, year = {2025}, author = {Crawford, MS and Ulu, A and Ramirez, BM and Santos, AN and Chatterjee, P and Canale, V and Manz, S and Lei, H and Soriano, SM and Nordgren, TM and McCole, DF}, title = {Respiratory Exposure to Agriculture Dust Extract Alters Gut Commensal Species and Key Metabolites in Mice.}, journal = {Journal of applied toxicology : JAT}, volume = {45}, number = {9}, pages = {1798-1810}, doi = {10.1002/jat.4808}, pmid = {40344252}, issn = {1099-1263}, support = {2R01DK091281/NH/NIH HHS/United States ; 1R01AI153314/NH/NIH HHS/United States ; 1R01DK130373/NH/NIH HHS/United States ; R00ES025819/NH/NIH HHS/United States ; R01HL158926/NH/NIH HHS/United States ; T34GM062756/NH/NIH HHS/United States ; U54OH007550//The University of California, Davis-Western Center for Agricultural Health and Safety/ ; //University of California Presidential Postdoctoral Fellowship Program/ ; //National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK)/ ; 2R01DK091281/NH/NIH HHS/United States ; 1R01AI153314/NH/NIH HHS/United States ; 1R01DK130373/NH/NIH HHS/United States ; R00ES025819/NH/NIH HHS/United States ; R01HL158926/NH/NIH HHS/United States ; T34GM062756/NH/NIH HHS/United States ; }, mesh = {Animals ; *Dust ; *Gastrointestinal Microbiome/drug effects ; Female ; Mice, Inbred C57BL ; Male ; Mice ; *Inhalation Exposure/adverse effects ; Feces/microbiology ; Swine ; Agriculture ; }, abstract = {Exposure to agricultural dust containing antimicrobial-resistant pathogens poses significant health risks for workers in animal agriculture production. Beyond causing severe airway inflammation, pollutants are linked to intestinal diseases. Swine farm dust is rich in ultrafine particles, gram-positive and gram-negative bacteria, and bacterial components such as lipopolysaccharides (LPS; endotoxins). In our previous study, we demonstrated that intranasal exposure of male and female C57BL/6J mice to 12.5% hog dust extract (HDE, containing 22.1-91.1 EU/mL) for 3 weeks resulted in elevated total cell and neutrophil counts in bronchoalveolar lavage fluid and increased intestinal permeability compared to saline controls. Now, we report that 16S and metagenomic analyses of Week 3 stool samples from HDE-treated mice indicate a reduced abundance of the beneficial species Akkermansia muciniphila and Clostridium sp. ASF356 and Lachnospiraceae bacterium. Bacterial alpha diversity showed increased species evenness in fecal samples from HDE-treated mice (Pielou's evenness, p = 0.047, n = 5-6/group). Metabolomic analysis also indicated significant reductions in key metabolites involved in energy metabolism, including riboflavin (p = 0.027, n = 11) and nicotinic acid (p = 0.049, n = 11), as well as essential amino acids, such as inosine (p = 0.043, n = 11) and leucine (p = 0.018, n = 11). While HDE exposure does not robustly alter overall microbial abundance or community structure, it leads to specific reductions in beneficial bacterial species and critical metabolites necessary for maintaining intestinal homeostasis by supporting energy metabolism, gut barrier function, microbiota balance, and immune regulation. The results of this study underscore the potential risks for gut health posed by inhalation of agricultural dust.}, } @article {pmid40343328, year = {2025}, author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G}, title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.}, journal = {Plant direct}, volume = {9}, number = {5}, pages = {e70078}, pmid = {40343328}, issn = {2475-4455}, abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.}, } @article {pmid40341642, year = {2025}, author = {Humińska-Lisowska, K and Michałowska-Sawczyn, M and Kosciolek, T and Łabaj, PP and Kochanowicz, A and Mieszkowski, J and Proia, P and Cięszczyk, P and Zielińska, K}, title = {Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16061}, pmid = {40341642}, issn = {2045-2322}, support = {2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; 2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Biomarkers/blood ; *Exercise/physiology ; Young Adult ; Feces/microbiology ; Exercise Test ; Athletes ; Anaerobiosis ; Adult ; }, abstract = {The gut microbiome influences physiological responses to exercise by modulating inflammatory markers and metabolite production. Athletes typically exhibit greater microbial diversity, which may be associated with improved performance, but the mechanisms linking different exercise modalities to the gut microbiome are not fully understood. In this study, blood and stool samples were collected from endurance athletes, strength athletes, and non-athletic controls performing two maximal exercise tests (the anaerobic Wingate test and the aerobic Bruce Treadmill Test) to integrate serum biomarker data with gut bacterial metagenomic profiles. While most biochemical markers showed similar post-exercise trends across groups, SPARC (secreted protein acidic and rich in cysteine) and adiponectin levels showed modality-specific responses. Strength-trained participants showed unique microbiome-biomarker associations after the Wingate test. In addition, baseline enrichment of certain bacterial taxa, including Clostridium phoceensis and Catenibacterium spp., correlated with reduced Bruce Treadmill test response in strength-trained individuals. These findings, while requiring further validation, indicate the complex interplay between exercise type, training background, and the gut microbiome, and suggest that specific microbial species may help shape recovery and adaptation.}, } @article {pmid40340756, year = {2025}, author = {Laue, HE and Willis, AD and Wang, F and MacDougall, MC and Xu, Y and Karagas, MR and Madan, JC and Fleisch, AF and Lanphear, BP and Cecil, KM and Yolton, K and Chen, A and Buckley, JP and Braun, JM}, title = {Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {50}, pmid = {40340756}, issn = {1756-994X}, support = {R35GM133420/GM/NIGMS NIH HHS/United States ; K99 ES034086/ES/NIEHS NIH HHS/United States ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; P30 ES013508/ES/NIEHS NIH HHS/United States ; R00 ES034086/ES/NIEHS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; Female ; Male ; Child ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Metagenomics/methods ; }, abstract = {BACKGROUND: The microbiome of adolescents is poorly understood, as are factors influencing its composition. We aimed to describe the healthy adolescent microbiome and identify early-life and concurrent predictors of its composition.

METHODS: We performed metagenomic sequencing of 247 fecal specimens from 167 adolescents aged 11-14 years participating in the Health Outcomes and Measures of the Environment (HOME) Study, a longitudinal pregnancy and birth cohort (Cincinnati, OH). We described common features of the adolescent gut microbiome and applied self-organizing maps (SOMs)-a machine-learning approach-to identify distinct microbial profiles (n = 4). Using prospectively collected data on sociodemographic characteristics, lifestyle, diet, and sexual maturation, we identified early-life and concurrent factors associated with microbial diversity and phylum relative abundance with linear regression models and composition with Kruskal-Wallis and Fisher's exact tests.

RESULTS: We found that household income and other sociodemographic factors were consistent predictors of the microbiome, with higher income associated with lower diversity and differential relative abundances of Firmicutes (increased) and Actinobacteria (decreased). Sexual maturation, distinct from chronological age, was related to higher diversity in females and differences in phylum relative abundances and compositional profiles in both males and females.

CONCLUSIONS: Our study suggests that adolescence is a unique window for gut microbial composition and that it may be shaped by both early-life and concurrent exposures, highlighting its potential in future epidemiologic research.}, } @article {pmid40340623, year = {2025}, author = {Deng, J and Zhang, J and Su, M and Li, J and Su, Y and Zhong, Q and Hu, J and Chen, Y and Liao, S and Lin, D and Guo, X}, title = {Fusobacterium mortiferum and its metabolite 5-aminovaleric acid promote the development of colorectal cancer in obese individuals through Wnt/β-catenin pathway by DKK2.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2502138}, pmid = {40340623}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology ; Animals ; Humans ; Mice ; Gastrointestinal Microbiome ; *Fusobacterium/metabolism ; *Wnt Signaling Pathway/drug effects ; *Obesity/microbiology/metabolism/complications ; *Intercellular Signaling Peptides and Proteins/metabolism/genetics ; Male ; Female ; Cell Line, Tumor ; Cell Proliferation ; Mice, Inbred C57BL ; }, abstract = {Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, with high incidence and mortality rates. An increasing body of research suggests that obesity is a significant risk factor for the development of CRC. Moreover, recent findings have highlighted the close association between the gut microbiota and both obesity and CRC. Despite this, the specific mechanisms by which the gut microbiota influences obesity and CRC remain unclear. This study aims to explore the role of the gut bacterium Fusobacterium mortiferum and its metabolite 5-aminovaleric acid (5-AVA) in the development of obesity and CRC. Our study found that the metabolite 5-aminovaleric acid produced by Fusobacterium mortiferum significantly inhibits the expression of the tumor suppressor DKK2. This inhibition leads to enhanced proliferation of CRC cells. Furthermore, we discovered that Fusobacterium mortiferum and 5-AVA can activate the Wnt/β-catenin signaling pathway by inhibiting DKK2, thereby promoting tumor growth. This finding was validated in CRC mouse models and in vitro experiments. Additional mechanistic studies revealed that 5-AVA interacts with the demethylase KDM6B, affecting the demethylation process of DKK2 and subsequently activating the Wnt/β-catenin signaling pathway. Our study retrospectively collected fecal samples from patients who underwent gastrointestinal endoscopy at the Sixth Affiliated Hospital of Sun Yat-sen University over the past five years. Participants were stratified into a healthy control group and an adenoma group based on the outcomes of their colonoscopies. Following this, we conducted metagenomic analysis to identify differential bacteria, and based on the results, we performed bacterial cultivation and metabolomic profiling. The roles of the targeted bacteria and their metabolites were further validated through animal models and cellular assays, employing techniques such as Western Blot, qPCR, immunohistochemistry, molecular docking simulations, and gene overexpression studies. This study uncovers the potential carcinogenic effects of Fusobacterium mortiferum and 5-AVA in the development of obesity and CRC. Our research emphasizes the complex interplay between the gut microbiota and host metabolism and suggests new directions for future research to explore how modulation of the gut microbiota could prevent and treat CRC.}, } @article {pmid40340458, year = {2025}, author = {Bay, L and Barnes, CJ and Fritz, BG and Ravnborg, N and Ruge, IF and Halling-Sønderby, A-S and Søeborg, SR and Langhoff, KH and Lex, C and Hansen, AJ and Thyssen, JP and Bjarnsholt, T}, title = {Unique dermal bacterial signature differentiates atopic dermatitis skin from healthy.}, journal = {mSphere}, volume = {10}, number = {6}, pages = {e0015625}, pmid = {40340458}, issn = {2379-5042}, support = {LF-OC-19-0003//LEO Fondet (LEO Foundation)/ ; LF17067//LEO Fondet (LEO Foundation)/ ; LF17067//LEO Fondet (LEO Foundation)/ ; }, mesh = {Humans ; *Dermatitis, Atopic/microbiology ; Adult ; *Microbiota ; Female ; Male ; *Skin/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Metagenomics ; Young Adult ; Epidermis/microbiology ; Case-Control Studies ; *Dermis/microbiology ; }, abstract = {UNLABELLED: Gaining a deeper understanding of the variation in skin microbiota across habitats and layers provides critical insights into the complex host-microbial interactions that drive inflammatory skin diseases. Our study investigated dermal versus epidermal microbiota in lesional and non-lesional skin of 37 adult atopic dermatitis (AD) patients and 37 healthy controls. Skin biopsies were partitioned into epidermal and dermal compartments, while serial tape strips collected the superficial epidermis. Bacterial communities were analyzed by cultivation, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confocal laser scanning microscopy, and metagenomic sequencing. We found that the effects of AD were evident across skin layers. The natural variation between skin layers and habitats diminishes in AD-affected skin, intensifying the impact of the microenvironment and host factors. A remarkably distinct dermal bacterial community was discovered among AD patients, being more conserved and providing a clearer difference between skin habitats, while the epidermis varied substantially. Importantly, comparisons between AD patients and controls revealed more genera differed when studying the dermal samples than the epidermal ones. Staphylococcus, Corynebacterium, and Cutibacterium genera differed with AD status across all samples, but Prevotella and Mitsuokella only differed in the dermis. In the dry and moist dermis, this translated into 14 and 61 gene pathways significantly varying with AD status, including many related to the biosynthesis of menaquinones (vitamin K2). These results suggest dermal sampling would allow for the role of the skin microbiome within AD pathogenesis to be better resolved since these communities are simpler and less prone to environmental contamination.

IMPORTANCE: This study sheds light on the profound impact of skin microbiota's complex composition and distribution in atopic dermatitis (AD). The distinctive bacterial profile and activity, especially within the dermal skin compartment, vividly mirrored the cutaneous conditions in this inflamed microenvironment. The striking similarity in bacterial communities across different skin habitats in atopic skin underscores the high influence of atopic dermatitis-the genetic predisposition to an amplified immune response. This finding suggests that the dermal bacterial profile could be a valuable tool for longitudinally monitoring changes during the disease's relapsing phases, allowing for a precise categorization of patients into specific AD endotypes. Broadening the focus throughout the entire eczema-affected skin paves the way for treatments capable of modulating dermal biological factors, offering more effective management of AD. By further centering the interest in host-microbial interactions, we can refine personalized treatments, ultimately improving the lives of millions suffering from atopic dermatitis.}, } @article {pmid40339893, year = {2025}, author = {Zhang, L and Wang, S and Jia, Y and Liu, Z and Yao, J and Chen, Y}, title = {Alterations in microbial communities and antibiotic resistance genes pre- and post-sludge bulking in a wastewater treatment plant.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {376}, number = {}, pages = {126391}, doi = {10.1016/j.envpol.2025.126391}, pmid = {40339893}, issn = {1873-6424}, mesh = {*Waste Disposal, Fluid/methods ; *Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; *Sewage/microbiology ; RNA, Ribosomal, 16S ; *Microbiota ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Sludge bulking is a common issue in wastewater treatment plants (WWTPs) that can disrupt microbial communities and potentially impact the abundance and spread of antibiotic resistance genes (ARGs) within treatment systems. This study employed high-throughput 16S rRNA gene sequencing and metagenomic sequencing to examine the changes in microbial communities and ARGs in a WWTP during non-bulking and bulking periods. The results indicated that bacterial diversity decreased in bulking sludge while maintaining a high removal efficiency of conventional pollutants. Significant differences were detected at the bacterial genus level between non-bulking and bulking sludge (p < 0.05). The proliferation of Candidatus_Microthrix contributed to sludge bulking, while Micropruina improved sludge settleability. When treating wastewater with the same water quality and quantity, anaerobic/anoxic/oxic (A[2]/O) exhibited the highest resistance to sludge bulking, followed by Bardenpho and the Carrousel oxidation ditch. The abundance of ARGs in bulking sludge (28.15-43.63 ppm) was lower than that in non-bulking sludge (51.72-59.01 ppm). The ARGs removal efficiency reached 96.24 % and 94.34 % during bulking and non-bulking periods, respectively. Network analysis revealed that Candidatus_Microthrix was positively correlated with aadS and tetX, and norank_f_Saprospiraceae exhibited positive correlations with vanRO and ANT(3″)-Iia. These findings provide valuable insights into the impacts of sludge bulking on WWTP performance and ARGs dynamics, informing evidence-based policies for sustainable wastewater treatment.}, } @article {pmid40339368, year = {2025}, author = {Zhang, X and Liu, T and Sun, W and Zhang, C and Jiang, X and You, X and Wang, X}, title = {The fate and ecological risk of typical diamide insecticides in soil ecosystems under repeated application.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138440}, doi = {10.1016/j.jhazmat.2025.138440}, pmid = {40339368}, issn = {1873-3336}, mesh = {*Insecticides/toxicity ; *Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; *ortho-Aminobenzoates/toxicity ; Ecosystem ; Soil/chemistry ; Nitrogen/metabolism ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; }, abstract = {Diamide insecticides are the third most widely used class of pesticides worldwide. However, the long-term impacts of repeated diamide applications on soil ecosystems remain unclear. This study investigated chlorantraniliprole (CLP) and cyantraniliprole (CYP) effects on soil ecosystems through simulated repeated exposures. Results showed both exhibited slow degradation in the soil, with repeated applications extending their persistence, particularly for CLP. Both significantly inhibited soil alkaline nitrogen and organic matter accumulation, while reducing urease and sucrase activities, with CLP exerting stronger inhibitory effects. Metagenomic analysis indicated that CLP and CYP notably reduced soil microbial diversity. Additionally, the two insecticides altered the soil microbial community structure and inhibited carbon-nitrogen metabolic pathways. Further analysis revealed that CLP treatment significantly decreased the relative abundances of Mesorhizobium and Marmoricola, whereas CYP treatment primarily reduced Clostridium_sensu_stricto_1. All of these genera exhibited significant positive correlations with key metabolic pathways in soil carbon and nitrogen cycling. Notably, the relative abundance of Sphingomonas increased significantly following CLP and CYP treatments, demonstrating potential degradation capabilities. Overall, both CLP and CYP posed ecological risks to soil ecosystems, with CLP exhibiting more severe impacts. These findings revealed the need for strengthened scientific management in actual production.}, } @article {pmid40338610, year = {2025}, author = {Gan, X and Yu, Q and Hu, X and Qian, Y and Mu, X and Li, H}, title = {Metagenomic and metatranscriptomic analysis reveals the enzymatic mechanism of plant polysaccharide degradation through gut microbiome in plateau model animal (Ochotona curzoniae).}, journal = {FEMS microbiology letters}, volume = {372}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf045}, pmid = {40338610}, issn = {1574-6968}, support = {32471575//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Polysaccharides/metabolism ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Lagomorpha/microbiology/metabolism ; *Bacteria/genetics/classification/metabolism/enzymology/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Glycoside Hydrolases/genetics/metabolism ; Transcriptome ; Poaceae/metabolism ; Altitude ; Gene Expression Profiling ; Cellulase/genetics/metabolism ; }, abstract = {Herbivorous animals can obtain energy by decomposing plant polysaccharides through gut microbiota, but the mechanism of gut microbiota decomposing plant polysaccharides in high-altitude model animals is still unclear. Plateau pika (Ochotona curzoniae) is a key model animal native to the Qinghai-Tibet Plateau with a high intake of grass. Thus, Plateau pika is an excellent animal model for studying how herbivorous animals digest and metabolize grass polysaccharides. Here, we used 16S rDNA, 16S rRNA, metagenomic, and metatranscriptomic sequencing to characterize gut microbial composition, gene potential, and expressed function in pikas from different altitudes. Unlike total bacteria, Oscillospira and Ruminococcus were main active bacterial genera in pika's gut. The metabolic pathways of cellulose and hemicellulose were up-regulated in the middle and high-altitude groups; those genes encoding polysaccharide enzymes were enriched. Notably, the proportion of lignin metabolic genes expressed in pika's gut was the highest, followed by cellulase and hemicellulase genes. According to comparative metagenomics of different animals, the number and relative abundance of cellulase and hemicellulase genes in pika's gut were at a higher level compared with steer, etc. These results indicated that plateau pika obtained sufficient energy from grass-based diet by increasing the expression of related metabolic enzymes.}, } @article {pmid40338094, year = {2025}, author = {Tanaka, M and Toyonaga, T and Nakagawa, F and Iwamoto, T and Hasegawa, Y and Komatsu, A and Sumiyoshi, N and Shibuya, N and Minemura, A and Ariyoshi, T and Matsumoto, A and Oka, K and Shimoda, M and Saruta, M}, title = {Dietary 3-aminobenzoic acid enhances intestinal barrier integrity and attenuates experimental colitis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {328}, number = {6}, pages = {G801-G810}, doi = {10.1152/ajpgi.00406.2024}, pmid = {40338094}, issn = {1522-1547}, support = {21K15985//Kaken Pharmaceutical (Kaken)/ ; }, mesh = {Humans ; Animals ; Caco-2 Cells ; *Intestinal Mucosa/metabolism/drug effects ; Mice ; Gastrointestinal Microbiome/drug effects ; Permeability/drug effects ; Male ; *Colitis, Ulcerative/metabolism/drug therapy ; Mice, Inbred C57BL ; Female ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism/drug effects/pathology ; }, abstract = {Disruption of intestinal epithelial integrity and increased permeability is central to the pathogenesis of ulcerative colitis (UC). In this study, we identified 3-aminobenzoic acid (3-ABA), a dietary component abundant in azuki beans, soybeans, and chickpeas as a regulator of epithelial permeability and inflammation in the colon. Screening 119 gut microbial metabolites revealed the ability of 4-ABA, a structural isomer of 3-ABA, to enhance barrier function in Caco2 cells. Further analysis of structural isomers identified 3-ABA as the most effective, significantly increasing transepithelial electrical resistance and reducing epithelial permeability. Using liquid chromatography-mass spectrometry, 3-ABA was detected in dietary beans and human fecal samples. Fecal 3-ABA levels were significantly lower in patients with UC compared with healthy individuals. Metagenomic and functional prediction analyses revealed dysbiosis in patients with UC, characterized by an enrichment of bacterial genes involved in ABA degradation. Gene expression analysis of 3-ABA-stimulated Caco2 cells demonstrated upregulation of tight junction molecules, such as CLDN1 and TJP1, enhancing epithelial barrier integrity. In a dextran sodium sulfate-induced colitis mouse model, rectal 3-ABA administration ameliorated colitis by enhancing epithelial barrier function and reducing inflammation. These findings highlight 3-ABA's potential as a dietary therapeutic agent for UC, offering a novel strategy to enhance intestinal integrity and mitigate inflammation.NEW & NOTEWORTHY Increased intestinal epithelial permeability is central to the pathogenesis of ulcerative colitis (UC). 3-Aminobenzoic acid (3-ABA), a dietary component abundant in beans, decreased epithelial permeability and attenuated colonic inflammation in a mouse experimental colitis model. Reduced fecal 3-ABA levels in patients with UC were associated with dysbiosis-driven accelerated degradation. These findings highlight the therapeutic potential of 3-ABA in UC by targeting colonic epithelium.}, } @article {pmid40335921, year = {2025}, author = {Jia, S and Mi, H and Su, Y and Liu, Y and Ming, Z and Lin, J}, title = {Changes of intestinal microbiome and its relationship with painful diabetic neuropathy in rats.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {281}, pmid = {40335921}, issn = {1471-2180}, support = {22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/microbiology/pathology ; Rats ; Male ; Rats, Sprague-Dawley ; Diabetes Mellitus, Experimental/microbiology/complications ; Interleukin-1beta/metabolism ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Tumor Necrosis Factor-alpha/metabolism ; Diabetes Mellitus, Type 2/microbiology/complications ; Colon/pathology/microbiology ; Spinal Cord/pathology/metabolism ; }, abstract = {OBJECTIVE: To analyze the gut bacterial microbiome in rats with painful diabetic neuropathy (PDN) compared to normal rats.

METHODS: Type 2 diabetes was induced in rats via a high-fat and high-sugar diet combined with a low dose of streptozotocin. Glucose metabolism and insulin sensitivity were evaluated using intraperitoneal glucose tolerance tests and insulin tolerance tests. The progression of peripheral neuropathy was assessed using the mechanical withdrawal threshold and thermal withdrawal latency. Histopathological analysis of rat colon tissues was performed using hematoxylin-eosin staining to observe morphological changes. The expression levels of pro-inflammatory cytokines TNF-α and IL-1β in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were then collected for metagenomic sequencing and analysis.

RESULT: Behavioral tests revealed reduced mechanical withdrawal threshold and thermal withdrawal latency in PDN rats. Histological analysis showed significant colonic mucosal damage and inflammatory cell infiltration, suggesting impaired intestinal barrier function. Elevated TNF-α and IL-1β levels in spinal cord tissues further highlight peripheral inflammation's role in PDN. Sequencing analysis revealed significant differences in gut microbiota composition between PDN and control rats, with altered Bacillota/Bacteroidota ratios and increased Lactobacillus abundance. Functional annotation analysis, based on the KEGG, EggNOG, and CAZy databases, indicated significant enrichment of metabolic pathways related to carbohydrate and amino acid metabolism, energy metabolism, and cell structure biogenesis in PDN rats. Cluster analysis identified higher functional clustering in Metabolism and Genetic Information Processing pathways in PDN rats.

CONCLUSION: This study demonstrates that PDN leads to altered gut microbiota composition, disrupted metabolic pathways, and increased inflammation, contributing to the pathological progression of diabetic neuropathy. This study provides new insights into the interplay between gut microbiota and diabetic neuropathy, offering potential avenues for therapeutic interventions targeting microbiome and metabolism.}, } @article {pmid40335750, year = {2025}, author = {Deepali, D and Tejoprakash, N and Sudhakara Reddy, M}, title = {Diversity of Bacterial Communities in Seleniferous Soils and Their Impact on Plant Growth and Selenium Toxicity.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {285}, pmid = {40335750}, issn = {1432-0991}, mesh = {*Selenium/toxicity/metabolism ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; *Soil/chemistry ; *Zea mays/growth & development/microbiology/drug effects ; Biodiversity ; *Microbiota ; Plant Roots/microbiology/growth & development ; *Soil Pollutants/toxicity ; Phylogeny ; }, abstract = {The present study aimed to investigate the diversity of bacterial communities in seleniferous soils using Illumina Mi-Seq Next-Generation Sequencing. This study also compared seleniferous soils (SE) with non-seleniferous (NS) soils to evaluate Selenium (Se) impact on microbial communities and soil properties. Metagenomic analysis identified Proteobacteria as the predominant phylum in both environments, with SE soils exhibiting a higher dominance (48%) than NS soils (31%). The most dominant operational taxonomic unit (OTU) across both soil types belonged to the genus Bacillus. Se altered microbial community composition, increasing the abundance of the Bacillaceae family (30%) and Pseudomonadaceae family (25%) compared to NS soil. Bacillus was the dominant genus in the SE environment indicating its tolerance to selenium. Diversity indices indicated that control soils had higher species richness, while SE soils exhibited a more stressed microbial structure. A consortium of bacterial isolates (Proteus terrae Se3, Halopseudomonas formosensis Se5, and Corynebacterium glutamicum Se38) was inoculated in maize plants cultivated in natural seleniferous soils. Plants inoculated with bacterial consortium grew more healthy and had greater biomass in their roots, shoots, and seeds. Bacterial inoculation results in lesser selenium accumulation in the roots, shoots and seeds of maize plants compared to non-inoculated plants. These results suggest that bacterial species from seleniferous soils may be employed as biofertilizers to enhance plant growth and help plants tolerate Se toxicity in seleniferous soils.}, } @article {pmid40335510, year = {2025}, author = {Zhi, J and Liang, Y and Zhao, W and Qiao, J and Zheng, Y and Peng, X and Li, L and Wei, X and Wang, W}, title = {Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {74}, pmid = {40335510}, issn = {2055-5008}, support = {82403470//National Natural Science Foundation of China/ ; 82401333//National Natural Science Foundation of China/ ; 21JCYBJC01570//Tianjin Municipal Science and Technology Committee/ ; 24JCQNJC01170//Tianjin Municipal Science and Technology Project/ ; TJWJ2023XK013//Tianjin Municipal Health Commission/ ; TJYXZDXK-046A//Tianjin Municipal Health Commission/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; *Microbiota ; Male ; Cross-Sectional Studies ; Middle Aged ; Female ; *Head and Neck Neoplasms/diagnosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Dysbiosis/microbiology ; *Mouth/microbiology ; Adult ; Biomarkers/analysis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Machine Learning ; Biomarkers, Tumor ; }, abstract = {Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.}, } @article {pmid40335465, year = {2025}, author = {Romano, S and Wirbel, J and Ansorge, R and Schudoma, C and Ducarmon, QR and Narbad, A and Zeller, G}, title = {Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4227}, pmid = {40335465}, issn = {2041-1723}, support = {BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; SEG 9093//European Molecular Biology Organization (EMBO)/ ; EMBO ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; 395357507 - SFB 1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Parkinson Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Machine Learning ; Metagenome ; }, abstract = {There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (4489 samples). Within most studies, microbiome-based machine learning models accurately classify PD patients (average AUC 71.9%). However, these models are study-specific and do not generalise well across other studies (average AUC 61%). Training models on multiple datasets improves their generalizability (average LOSO AUC 68%) and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Moreover, meta-analysis of shotgun metagenomes delineates PD-associated microbial pathways potentially contributing to gut health deterioration and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, microbial pathways for solvent and pesticide biotransformation are enriched in PD. These results align with epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbes modulate their toxicity. Here, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.}, } @article {pmid40335388, year = {2025}, author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R}, title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.004}, pmid = {40335388}, issn = {1878-4372}, abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.}, } @article {pmid40334798, year = {2025}, author = {Zhu, X and Chen, L and Yang, P and Luo, S and Teng, M and Zhu, W and Li, Y and Zhao, D and Wang, N and Chen, X and Cheng, M and Tu, H and Huang, W and Yang, F and Wang, L and Liu, X and Ning, K}, title = {Microbiome catalog and dynamics of the Chinese liquor fermentation process.}, journal = {Bioresource technology}, volume = {431}, number = {}, pages = {132620}, doi = {10.1016/j.biortech.2025.132620}, pmid = {40334798}, issn = {1873-2976}, mesh = {*Fermentation ; *Microbiota/genetics ; *Alcoholic Beverages/microbiology ; Multigene Family ; China ; Bacillus licheniformis/genetics/metabolism ; }, abstract = {Fermented food remains poorly understood, largely due to the lack of knowledge about microbes in food fermentation. Here, this study constructed Moutai Fermented Grain Catalog (MTFGC), a representative liquor fermented by one of the most complex fermentations. MTFGC comprised 8,379,551 non-redundant genes and 5,159 metagenome-assembled genomes, with 20% species and 20% genes being novel. Additionally, 25,625 biosynthetic gene clusters (BGCs) and 28 BGC-enriched species were identified. Moreover, the microbial community assembly was deterministic, with significant species and gene changes in early fermentation stages, while stabilizing in later stages. Further BGC-knockout experiments verified Bacillus licheniformis, a BGC-enriched species, employed its BGCs for synthesizing the aroma-related lipopeptide lichenysin. This study has established the largest genetic resource for fermented food, uncovering its uniqueness and high metabolic potential. These findings facilitate the transition potential from traditional fermentation to precision-driven synthetic biology in food systems.}, } @article {pmid40333159, year = {2025}, author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F}, title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333159}, issn = {2076-0817}, support = {22LCYY-QH10//Jinling Hospital/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; *Psoriasis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.}, } @article {pmid40333054, year = {2025}, author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and da Silva, MS and Weber, MN and de Barros, MP and Spilki, FR}, title = {Virome of Terrestrial Mammals and Bats from Southern Brazil: Circulation of New Putative Members of the Togaviridae Family and Other Findings.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40333054}, issn = {2076-0817}, support = {405786/2022-0//CNPQ/ ; }, mesh = {Animals ; Brazil/epidemiology ; *Chiroptera/virology ; *Virome ; *Mammals/virology ; Phylogeny ; Metagenomics ; Humans ; }, abstract = {The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic sequencing. Akodon montensis (n = 15 individuals) and Coendou spinosus (n = 4) harbored Chikungunya virus (ChikV, Togaviridae), marking its first detection in these hosts. Molossus molossus (n = 17) presented Coronaviridae and Orthoherpesviridae, while Eptesicus furinalis (n = 1) also carried Coronaviridae. A broad virome diversity, including Togaviridae and Adenoviridae members, was identified in Didelphis albiventris (n = 43), with significant relevance to human health. Additional species, such as Callithrix jacchus (n = 1), Leopardus guttulus (n = 1), Myocastor coypus (n = 1), Monodelphis iheringi (n = 1), Thaptomys nigrita (n = 1), Sooretamys angouya (n = 1), Brucepattersonius iheringi (n = 1), and Lasiurus blossevillii (n = 1), contributed to insights into viral reservoirs. These results underscore the importance of virome studies in regions harboring high biodiversity, emphasizing genomic surveillance as a vital tool for monitoring zoonotic viruses and safeguarding global health.}, } @article {pmid40330019, year = {2025}, author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S}, title = {Investigation of dynamic microbial migration patterns in the respiratory tract.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1542562}, pmid = {40330019}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.

METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.

RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.

CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.}, } @article {pmid40329496, year = {2025}, author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B}, title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.}, journal = {Journal of forensic sciences}, volume = {70}, number = {4}, pages = {1261-1273}, pmid = {40329496}, issn = {1556-4029}, mesh = {Animals ; *Postmortem Changes ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Swine ; *Specimen Handling/methods ; *Immersion ; DNA, Bacterial ; *Water Microbiology ; Models, Animal ; *Bone and Bones/microbiology ; }, abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).}, } @article {pmid40329426, year = {2025}, author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M}, title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {115}, pmid = {40329426}, issn = {2049-2618}, support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota/genetics ; Female ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Male ; Adult ; Metagenomics/methods ; *Oropharynx/microbiology ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Family Characteristics ; Young Adult ; Metagenome ; }, abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.

RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.

CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.}, } @article {pmid40329425, year = {2025}, author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M}, title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {48}, pmid = {40329425}, issn = {2524-6372}, support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.

RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.

CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.}, } @article {pmid40329386, year = {2025}, author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y}, title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {114}, pmid = {40329386}, issn = {2049-2618}, support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; }, mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; }, abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.}, } @article {pmid40328980, year = {2025}, author = {Liébana-García, R and López-Almela, I and Olivares, M and Romaní-Pérez, M and Manghi, P and Torres-Mayo, A and Tolosa-Enguís, V and Flor-Duro, A and Bullich-Vilarrubias, C and Rubio, T and Rossini, V and Segata, N and Sanz, Y}, title = {Gut commensal Phascolarctobacterium faecium retunes innate immunity to mitigate obesity and metabolic disease in mice.}, journal = {Nature microbiology}, volume = {10}, number = {6}, pages = {1310-1322}, pmid = {40328980}, issn = {2058-5276}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Obesity/immunology/microbiology ; *Immunity, Innate ; Mice ; Humans ; *Metabolic Diseases/immunology/microbiology ; Male ; Macrophages/immunology ; Female ; Mice, Inbred C57BL ; Symbiosis ; Disease Models, Animal ; Metagenome ; }, abstract = {The gut microbiota may protect against obesity and chronic metabolic conditions by regulating the immune response to dietary triggers. Yet the specific bacteria that control the overactivation of the immune system in obesity and their mode of action remain largely unknown. Here we surveyed 7,569 human metagenomes and observed an association between the gut symbiont Phascolarctobacterium faecium and non-obese adults regardless of nationality, sex or age. In a mouse model of diet-induced obesity, we confirmed the specificity of P. faecium DSM 32890 anti-obesogenic properties compared with other species of the same genus. P. faecium reversed the inflammatory phenotype associated with obesity. Specifically, P. faecium promoted polarization of alternatively activated macrophages (M2), which reversed the obesity-induced increase in gut-resident type 1 innate lymphoid cells. This resulted in mitigation of glucose intolerance, adiposity and body weight gain irrespective of treatment with live or pasteurized bacteria. The metabolic benefits were independent of the adaptive immune system, but they were abolished by an inhibitor of M2 polarization in mice. P. faecium directly promoted M2-macrophage polarization through TLR2 signalling and these effects seemed to be independent of gut microbiota changes. Overall, we identify a previously undescribed gut commensal bacterium that could help mitigate obesity and metabolic comorbidities by retuning the innate immune response to hypercaloric diets.}, } @article {pmid40328944, year = {2025}, author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE}, title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.}, journal = {Nature microbiology}, volume = {10}, number = {5}, pages = {1184-1197}, pmid = {40328944}, issn = {2058-5276}, support = {R35 GM149270/GM/NIGMS NIH HHS/United States ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 GM130777/GM/NIGMS NIH HHS/United States ; R01DK121822//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21 AI154075/AI/NIAID NIH HHS/United States ; R35 GM141861/GM/NIGMS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35 GM143056/GM/NIGMS NIH HHS/United States ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 DK121822/DK/NIDDK NIH HHS/United States ; R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Microbiota/genetics ; Feces/microbiology ; Female ; *Metagenomics/methods ; Bayes Theorem ; Longitudinal Studies ; Escherichia coli/genetics/isolation & purification/classification ; Infant ; Algorithms ; Enterococcus faecalis/genetics/isolation & purification/classification ; Adult ; *Bacteria/genetics/classification/isolation & purification ; }, abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.}, } @article {pmid40328731, year = {2025}, author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y}, title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4211}, pmid = {40328731}, issn = {2041-1723}, support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Insulin Resistance/physiology ; Female ; *Bile Acids and Salts/metabolism ; Blood Glucose/metabolism ; Postprandial Period ; Insulin/blood/metabolism ; Double-Blind Method ; Aged ; *Dietary Fats, Unsaturated/administration & dosage ; Feces/microbiology/chemistry ; Adult ; Prediabetic State/metabolism/diet therapy/microbiology ; }, abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.}, } @article {pmid40328090, year = {2025}, author = {Xia, Y and Lan, Y and Xu, Y and Liu, F and Chen, X and Luo, J and Xu, H and Liu, Y}, title = {Effects of microplastics and tetracycline induced intestinal damage, intestinal microbiota dysbiosis, and antibiotic resistome: metagenomic analysis in young mice.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109512}, doi = {10.1016/j.envint.2025.109512}, pmid = {40328090}, issn = {1873-6750}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; *Anti-Bacterial Agents/toxicity ; *Tetracycline/toxicity ; *Dysbiosis/chemically induced ; Metagenomics ; *Intestines/drug effects ; *Drug Resistance, Microbial/genetics ; }, abstract = {Microplastics (MPs) and antibiotic tetracycline (TC) are widespread in the environment and constitute emerging combined contaminants. Young individuals are particularly vulnerable to agents that disrupt intestinal health and development. However, the combined effects of MPs and TC remain poorly understood. In this study, we developed a young mouse model exposed to polystyrene MPs, either alone or in combination with TC for 8 weeks to simulate real-life dietary exposure during early life. Our findings revealed that concurrent exposure to MPs and TC caused the most severe intestinal barrier dysfunction driven by inflammatory activation and oxidative imbalance. Moreover, exposure to MPs and TC reduced the abundance of potential probiotics while promoting the growth of opportunistic pathogens. Metagenomic analysis further indicated that co-exposure to MPs and TC enhanced the abundance of bacteria carrying either antibiotic resistance genes (ARGs) or virulence factor genes (VFGs), contributing to the widespread dissemination of potentially harmful genes. Finally, a strong positive correlation was observed between microbiota dysbiosis, ARGs, and VFGs. In general, this study highlighted the hazards of MPs and antibiotics to intestinal health in young mice, which provided a new perspective into the dynamics of pathogens, ARGs, and VFGs in early-life intestinal environments.}, } @article {pmid40327993, year = {2025}, author = {Grafakou, ME and Pferschy-Wenzig, EM and Aziz-Kalbhenn, H and Kelber, O and Moissl-Eichinger, C and Bauer, R}, title = {Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {187}, number = {}, pages = {118111}, doi = {10.1016/j.biopha.2025.118111}, pmid = {40327993}, issn = {1950-6007}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Hypericum/chemistry ; *Plant Extracts/pharmacology ; *Brain/drug effects/metabolism ; Male ; Adult ; Female ; Feces/microbiology ; Antidepressive Agents/pharmacology ; *Brain-Gut Axis/drug effects ; }, abstract = {Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.}, } @article {pmid40327666, year = {2025}, author = {Yang, X and Zhang, Y and Xu, Y and Xu, Y and Zhang, M and Guan, Q and Hu, W and Tun, HM and Xia, Y}, title = {Microbial Disturbances Caused by Pesticide Exposure and Their Predictive Implications for Gestational Diabetes Mellitus.}, journal = {Environmental science & technology}, volume = {59}, number = {19}, pages = {9449-9460}, doi = {10.1021/acs.est.5c01076}, pmid = {40327666}, issn = {1520-5851}, mesh = {Female ; *Diabetes, Gestational ; Pregnancy ; Humans ; *Pesticides ; *Gastrointestinal Microbiome/drug effects ; Adult ; RNA, Ribosomal, 16S ; Biomarkers ; }, abstract = {Previous studies have suggested that pesticide exposure and gut microbiome alterations are associated with gestational diabetes mellitus (GDM) risk. Understanding the complex interactive effect of these factors on GDM is essential. In a cohort of 852 pregnant women, we assessed pesticide levels in serum and analyzed the gut microbiota using 16S rRNA and shotgun metagenomic sequencing. We explored the interactions between pesticides and gut microbiota, assessed their roles in GDM development, and proposed a predictive model based on identified biomarkers. We identified an environmental risk score (ERS), denoting the pesticide mixture level significantly associated with GDM, with the gut microbiota, particularly involving the Dorea branch, playing a crucial mediating role. In addition, we found an interactive effect of pesticide exposure and gut microbiota on GDM risk. Notably, low Prevotella enrichment combined with high ERS arisen from pesticide levels led to a 10.36-fold increased GDM risk. The identified pesticide and gut microbial biomarkers achieved high predictive accuracy for GDM (AUC: 0.833, 95% CI: 0.748-0.918). Collectively, maternal pesticide exposure may induce disrupted microbiome-dependent glycemic alteration, necessitating future assessment of clinical implications. Potential GDM markers can serve as targets for therapeutic intervention caused by pesticides, leading to prevention.}, } @article {pmid40327160, year = {2025}, author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z}, title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {282}, pmid = {40327160}, issn = {1432-0991}, support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal & Child Research Fund Project" of Biostime Institute of Nutrition & Care/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.}, } @article {pmid40326765, year = {2025}, author = {Lindner, BG and Graham, KE and Phaneuf, JR and Hatt, JK and Konstantinidis, KT}, title = {SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.}, journal = {Environmental science & technology}, volume = {59}, number = {19}, pages = {9507-9516}, pmid = {40326765}, issn = {1520-5851}, mesh = {*Feces/microbiology ; *Metagenomics ; Animals ; *Microbiota ; Metagenome ; }, abstract = {Methodologies utilizing metagenomics are attractive to fecal source tracking (FST) aims for assessing the presence and proportions of various fecal inputs simultaneously. Yet, compared to established culture- or PCR-based techniques, metagenomic approaches for these purposes are rarely benchmarked or contextualized for practice. We performed shotgun sequencing experiments (n = 35) of mesocosms constructed from the water of a well-studied recreational and drinking water reservoir spiked with various fecal (n = 6 animal sources, 3 wastewater sources, and 1 septage source) and synthetic microbiome spike-ins (n = 1) introduced at predetermined cell concentrations to simulate fecal pollution events of known composition. We built source-associated genome databases using publicly available reference genomes and metagenome assembled genomes (MAGs) recovered from short- and long-read sequencing of the fecal spike-ins, and then created an associated bioinformatic tool, called SourceApp, for inferring source attribution and apportionment by mapping the metagenomic data to these genome databases. SourceApp's performance varied substantially by source, with cows being underestimated due to under sampling of cow fecal microbiomes. Parameter tuning revealed sensitivity and specificity near 0.90 overall, which exceeded all alternative tools. SourceApp can assist researchers with analyzing and interpreting shotgun sequencing data and developing standard operating procedures on the frontiers of metagenomic FST.}, } @article {pmid40326511, year = {2025}, author = {Zhu, Y and Liu, Q and Alffenaar, JW and Wang, S and Cao, J and Dong, S and Zhou, X and Li, X and Li, X and Xiong, H and Zhu, L and Hu, Y and Wang, W}, title = {Gut Microbiota in Patients with Tuberculosis Associated with Different Drug Exposures of Antituberculosis Drugs.}, journal = {Clinical pharmacology and therapeutics}, volume = {118}, number = {1}, pages = {252-262}, doi = {10.1002/cpt.3687}, pmid = {40326511}, issn = {1532-6535}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-03//Shanghai New Three-year Action Plan for Public Health/ ; 82073612//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antitubercular Agents/pharmacokinetics/therapeutic use/administration & dosage ; Male ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis, Pulmonary/drug therapy/microbiology ; Rifampin/pharmacokinetics ; Cohort Studies ; Pyrazinamide/pharmacokinetics ; Aged ; Metagenomics ; Isoniazid/pharmacokinetics ; }, abstract = {Interindividual variability in drug exposure can significantly influence treatment outcomes and may lead to drug concentration-related side effects during tuberculosis (TB) treatment. Although the gut microbiota is known to affect drug metabolism, its impact on anti-TB drugs has not been thoroughly explored. This study sought to elucidate the relationship between pre-treatment gut microbiota and drug exposure levels among patients with pulmonary TB. Two cohorts were analyzed: a discovery cohort (N = 99) and a validation cohort (N = 32), both comprising patients undergoing anti-TB therapy with rifampicin, isoniazid, pyrazinamide, and ethambutol. The gut microbiota patterns of participants from the discovery cohort and the validation cohort were profiled by 16S rRNA gene sequencing and metagenomics, respectively. Analyses of both cohorts robustly established a positive association between pre-treatment microbial diversity and drug exposure, as well as significant differences in gut microbiota composition across various drug exposure groups. At the species level, Faecalibacterium prausnitzii was positively associated with drug exposure to rifampicin. Moreover, functional analysis revealed that starch and sucrose metabolism and secondary bile acid biosynthesis were more abundant in the high drug exposure group. To identify biomarkers capable of stratifying patients based on their drug exposure levels, 11 taxa, represented by Faecalibacterium, were selected in the discovery cohort (AUC = 0.992) and were confirmed in the validation cohort with high predictive accuracy (AUC = 0.894). This study demonstrated a correlation between microbial dysbiosis and reduced exposure to anti-TB medications. Optimizing treatment by regulating gut microbiota to improve drug exposure levels requires further validation through larger scale multicenter clinical trials.}, } @article {pmid40325896, year = {2025}, author = {Ikegwuoha, NPP and Hanekom, T and Booysen, E and Jason, C and Parker-Nance, S and Davies-Coleman, MT and van Zyl, LJ and Trindade, M}, title = {Fimsbactin Siderophores From a South African Marine Sponge Symbiont, Marinomonas sp. PE14-40.}, journal = {Microbial biotechnology}, volume = {18}, number = {5}, pages = {e70155}, pmid = {40325896}, issn = {1751-7915}, support = {//South African Medical Research Council (Self-Initiated grant)/ ; 87326//DSI/NRF SARChI research chair in Microbial Genomics/ ; 312184//European Union PharmaSea Consortium/ ; 129660//National Research Foundation/ ; }, mesh = {*Siderophores/chemistry/metabolism/genetics/isolation & purification ; Multigene Family ; Animals ; Biosynthetic Pathways/genetics ; *Porifera/microbiology ; Symbiosis ; Hydroxamic Acids/metabolism/chemistry ; }, abstract = {Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1-6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.}, } @article {pmid40325616, year = {2025}, author = {Xu, HY and Jiang, MT and Yang, YF and Huang, Y and Yang, WD and Li, HY and Wang, X}, title = {Microalgae-Based Fucoxanthin Attenuates Rheumatoid Arthritis by Targeting the JAK-STAT Signaling Pathway and Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {19}, pages = {11708-11719}, doi = {10.1021/acs.jafc.4c12474}, pmid = {40325616}, issn = {1520-5118}, mesh = {*Xanthophylls/administration & dosage ; *Arthritis, Rheumatoid/drug therapy/microbiology/genetics/metabolism/immunology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Signal Transduction/drug effects ; Animals ; *Microalgae/chemistry ; Mice ; Male ; *Janus Kinases/genetics/metabolism/immunology ; *STAT Transcription Factors/genetics/metabolism/immunology ; *Diatoms/chemistry ; }, abstract = {Fucoxanthin, an abundant carotenoid in marine algae, has garnered attention for its diverse health benefits, including anti-inflammatory and anticancer properties. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation and damage. This study investigated the therapeutic potential of fucoxanthin extracted from Phaeodactylum tricornutum in collagen-induced RA. Our results demonstrated that fucoxanthin significantly alleviated RA symptoms, including weight loss, joint swelling, and decreased appetite. Histological analysis revealed that fucoxanthin mitigated synovial inflammation, cartilage damage, and bone erosion. Mechanistically, transcriptomic analysis and cell experiments indicated that fucoxanthin suppressed the JAK-STAT signaling pathway by downregulating the expression of inflammatory cytokines, such as IL-6 and IL-1β. Furthermore, metagenomic analysis suggested that fucoxanthin restored the altered gut microbiota composition associated with RA. These findings highlight the therapeutic potential of fucoxanthin from P. tricornutum in the management of RA by targeting multiple pathways, including inflammation and gut microbiota.}, } @article {pmid40325116, year = {2025}, author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S}, title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15683}, pmid = {40325116}, issn = {2045-2322}, support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; }, mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation & purification/genetics ; }, abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.}, } @article {pmid40324646, year = {2025}, author = {Shen, H and Wang, D and Huang, Y and Yang, Y and Ji, S and Zhu, W and Liu, Q}, title = {2,3,7,8-tetrachlorodibenzofuran modulates intestinal microbiota and tryptophan metabolism in mice.}, journal = {Life sciences}, volume = {373}, number = {}, pages = {123679}, doi = {10.1016/j.lfs.2025.123679}, pmid = {40324646}, issn = {1879-0631}, mesh = {Animals ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Polychlorinated Dibenzodioxins/toxicity ; Mice, Inbred C57BL ; Environmental Pollutants/toxicity ; Indoles/metabolism/pharmacology ; Intestinal Mucosa/metabolism/drug effects ; *Benzofurans/toxicity ; }, abstract = {Persistent organic pollutants (POPs) are known to disrupt gut microbiota composition and host metabolism, primarily through dietary exposure. In this study, we investigate the impact of 2,3,7,8-tetrachlorodibenzofuran (TCDF) on gut microbiota and host metabolic processes. RNA-seq analysis revealed that TCDF exposure significantly affected tryptophan metabolism, lipid metabolic pathways, and immune system function. Metagenomic and metabolomic analyses further showed that TCDF reduced the abundance of Mucispirillum schaedleri and levels of two key tryptophan metabolites, indole-3-carboxaldehyde (3-IAld) and Indole acrylic acid (IA). Supplementation with 3-IAld and IA alleviated TCDF-induced liver toxicity in mouse, as evidenced by reduced Cyp1a1 expression, and mitigated intestinal inflammation, reflected by lower pro-inflammatory cytokines (Ifn-γ and Il-1β) in the colon. Additionally, 3-IAld and IA supplementation enhanced intestinal barrier function, as demonstrated by increased Mucin 2 (MUC2) expression in the gut mucosa of mouse. These findings suggest that TCDF exposure disrupts the gut microbiome and host metabolic balance, and highlight the potential therapeutic role of tryptophan-derived metabolites in mitigating environmental pollutant-induced damage.}, } @article {pmid40323477, year = {2025}, author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG}, title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.}, journal = {Medical oncology (Northwood, London, England)}, volume = {42}, number = {6}, pages = {195}, pmid = {40323477}, issn = {1559-131X}, mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; }, abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.}, } @article {pmid40323435, year = {2025}, author = {Reynolds, J and Yoon, JY}, title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.}, journal = {Mikrochimica acta}, volume = {192}, number = {6}, pages = {334}, pmid = {40323435}, issn = {1436-5073}, mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; }, abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.}, } @article {pmid40322835, year = {2025}, author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C}, title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {93}, number = {5}, pages = {e70082}, doi = {10.1111/aji.70082}, pmid = {40322835}, issn = {1600-0897}, support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; }, abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.

METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.

RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-κB, MMP3, IκBα, IL-1β, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.

CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.}, } @article {pmid40321823, year = {2025}, author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A}, title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19305}, pmid = {40321823}, issn = {2167-8359}, mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Islands ; *Fungi/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Ecosystem ; *Microbiota ; }, abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.}, } @article {pmid40320901, year = {2025}, author = {Gervasoni, KN and Iacia, MVMS and Silva, KO and Franco, LG and Mendes, MEF and Neves, TJDC and Sanches, WS and Oliveira, LB and Saito, EA and Vieira, KCO and Pereira, VC and Nai, GA and Winkelstroter, LK}, title = {Protective Effect of Piperine on Indomethacin-Induced Intestinal Damage.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {12}, pages = {e70097}, doi = {10.1002/mnfr.70097}, pmid = {40320901}, issn = {1613-4133}, mesh = {Animals ; *Polyunsaturated Alkamides/pharmacology ; *Piperidines/pharmacology ; *Alkaloids/pharmacology ; *Benzodioxoles/pharmacology ; Male ; *Indomethacin/adverse effects/toxicity ; Mice ; Gastrointestinal Microbiome/drug effects ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Intestine, Small/drug effects/pathology ; Intestinal Mucosa/drug effects/pathology ; Aspartate Aminotransferases/blood ; Protective Agents/pharmacology ; Intestines/drug effects/pathology ; }, abstract = {Nonsteroidal antiinflammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammation and chronic pain. Chronic use of NSAIDs is associated with adverse events and organ damage, especially to the gastric mucosa and small intestine. This study evaluates the protective effect of piperine on indomethacin-induced intestinal damage. Eighteen male Mus musculus mice, aged 6-8 weeks, were used. Intestinal damage was induced with indomethacin (10 mg/mL) and cotreatment with piperine (20 mg/mL), both administered orally. After 14 days, the animals were euthanized. Biochemical serological analysis was performed. Intestinal inflammation was assessed based on macroscopic, histopathological, and metagenomic analyses. Histopathological analysis showed a reduction in small intestine inflammation (p < 0.05) and the disappearance of necrosis in the intestinal wall of the large intestine. Crypt and villus measurements showed increased values in the piperine-treated group (p < 0.05). An approximately six-fold increase in aspartate aminotransferase (AST) was observed in the Indomethacin group (p < 0.05). Regarding the intestinal microbiota, an increase in genus diversity was observed in the piperine-treated group (p < 0.05). There was a 50% reduction in micronucleus formation with the administration of piperine 20 mg/kg (p < 0.05). It was concluded that cotreatment with piperine has great potential in mitigating the side effects caused by NSAIDs.}, } @article {pmid40320520, year = {2025}, author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J}, title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {111}, pmid = {40320520}, issn = {2049-2618}, support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; }, mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Droughts ; }, abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.}, } @article {pmid40318372, year = {2025}, author = {Chu, D and Zhang, H and Wang, Z and Ning, K}, title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.}, journal = {The Science of the total environment}, volume = {980}, number = {}, pages = {179522}, doi = {10.1016/j.scitotenv.2025.179522}, pmid = {40318372}, issn = {1879-1026}, mesh = {*Ecosystem ; *Fresh Water/microbiology ; China ; *Water Microbiology ; *Microbiota ; Bacteria ; Metagenome ; Lakes/microbiology ; *Environmental Monitoring ; }, abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.}, } @article {pmid40318224, year = {2025}, author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ}, title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40318224}, issn = {1751-7370}, mesh = {Animals ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Sea Cucumbers/physiology ; *Coral Reefs ; *Anthozoa/microbiology ; *Microbiota ; Polynesia ; Metagenomics ; Metagenome ; Bacteria/classification/genetics/metabolism ; }, abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increased coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.}, } @article {pmid40316630, year = {2025}, author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD}, title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15356}, pmid = {40316630}, issn = {2045-2322}, support = {Small grant//Universidad del Rosario/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; }, abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.}, } @article {pmid40315837, year = {2025}, author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD}, title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.}, journal = {Cell host & microbe}, volume = {33}, number = {5}, pages = {643-656.e7}, pmid = {40315837}, issn = {1934-6069}, support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *Staphylococcus epidermidis/genetics/isolation & purification/classification ; *Propionibacterium acnes/genetics/isolation & purification/classification ; Adult ; Metagenome ; Genome, Bacterial ; Phylogeny ; Male ; Skin Microbiome ; }, abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.}, } @article {pmid40315739, year = {2025}, author = {Ma, G and Yang, P and Lu, T and Deng, X and Meng, L and Xie, H and Zhou, J and Xiao, X and Tang, X}, title = {Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.}, journal = {Journal of reproductive immunology}, volume = {169}, number = {}, pages = {104535}, doi = {10.1016/j.jri.2025.104535}, pmid = {40315739}, issn = {1872-7603}, mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Young Adult ; *Bacteria/genetics ; }, abstract = {AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.

METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.

RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.

CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.}, } @article {pmid40315414, year = {2025}, author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ}, title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1012268}, pmid = {40315414}, issn = {1553-7358}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; *Viruses/genetics/classification ; Computational Biology/methods ; Feces/virology ; Metagenome/genetics ; Infant ; Databases, Genetic ; }, abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.}, } @article {pmid40314681, year = {2025}, author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q and Li, L}, title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.}, journal = {The new microbiologica}, volume = {48}, number = {1}, pages = {46-59}, pmid = {40314681}, issn = {1121-7138}, mesh = {Humans ; *Bibliometrics ; *Biomedical Research ; Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.}, } @article {pmid40313603, year = {2025}, author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y}, title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.}, journal = {Phenomics (Cham, Switzerland)}, volume = {5}, number = {1}, pages = {76-90}, pmid = {40313603}, issn = {2730-5848}, abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.}, } @article {pmid40313461, year = {2025}, author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R}, title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1543100}, pmid = {40313461}, issn = {2235-2988}, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; }, abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.}, } @article {pmid40313234, year = {2025}, author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N}, title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.}, journal = {Journal of dietary supplements}, volume = {22}, number = {4}, pages = {511-524}, doi = {10.1080/19390211.2025.2498127}, pmid = {40313234}, issn = {1939-022X}, mesh = {Humans ; *Prebiotics/administration & dosage ; *Crohn Disease/microbiology/therapy/drug therapy ; Pilot Projects ; Female ; Male ; Feces/microbiology/chemistry ; Double-Blind Method ; Adult ; *Dietary Supplements ; *Agaricales/chemistry ; Gastrointestinal Microbiome ; Middle Aged ; Leukocyte L1 Antigen Complex/analysis ; C-Reactive Protein/analysis ; Treatment Outcome ; Young Adult ; }, abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.}, } @article {pmid40312907, year = {2025}, author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ}, title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.}, journal = {Investigative and clinical urology}, volume = {66}, number = {3}, pages = {272-280}, pmid = {40312907}, issn = {2466-054X}, support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; }, mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; }, abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.}, } @article {pmid40311618, year = {2025}, author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N}, title = {Global genetic diversity of human gut microbiome species is related to geographic location and host health.}, journal = {Cell}, volume = {188}, number = {15}, pages = {3942-3959.e9}, doi = {10.1016/j.cell.2025.04.014}, pmid = {40311618}, issn = {1097-4172}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Phylogeny ; Metagenome/genetics ; Male ; Female ; Bile Acids and Salts/blood ; Clostridiales ; }, abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.}, } @article {pmid40311598, year = {2025}, author = {Hong, Y and Cui, J and Xu, G and Li, N and Peng, G}, title = {Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {142}, number = {}, pages = {156656}, doi = {10.1016/j.phymed.2025.156656}, pmid = {40311598}, issn = {1618-095X}, mesh = {Animals ; *Asthma/drug therapy/microbiology ; *T-Lymphocytes, Regulatory/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; Mice, Inbred C57BL ; *Interleukin-17/metabolism/genetics ; Mice ; Histones/metabolism ; Cell Differentiation/drug effects ; Male ; Acetylation ; Disease Models, Animal ; Histone Deacetylases/metabolism ; Lung/drug effects/pathology ; }, abstract = {BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.

PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.

METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.

RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.

CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.}, } @article {pmid40310938, year = {2025}, author = {Ma, WJ and Wang, C and Kothandapani, J and Luzentales-Simpson, M and Menzies, SC and Bescucci, DM and Lange, ME and Fraser, ASC and Gusse, JF and House, KE and Moote, PE and Xing, X and Grondin, JM and Hui, BW and Clarke, ST and Shelton, TG and Haskey, N and Gibson, DL and Martens, EC and Abbott, DW and Inglis, GD and Sly, LM and Brumer, H}, title = {Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6754}, pages = {1410-1416}, doi = {10.1126/science.adk7633}, pmid = {40310938}, issn = {1095-9203}, mesh = {Animals ; Humans ; Mice ; *Anti-Inflammatory Agents/administration & dosage ; Bacteria/enzymology/metabolism ; Dietary Fiber/metabolism ; *Drug Delivery Systems/methods ; *Gastrointestinal Microbiome ; *Glycoconjugates/chemistry/administration & dosage ; Glycoside Hydrolases/metabolism ; *Inflammatory Bowel Diseases/drug therapy/microbiology ; *Oligosaccharides/chemistry ; }, abstract = {The gut microbiota of mammals possess distinctive metabolic pathways with untapped therapeutic potential. Using molecular insights into dietary fiber metabolism by the human gut microbiota, we designed a targeted drug delivery system, called GlycoCaging, that is based on bespoke glycoconjugates of a complex plant oligosaccharide. GlycoCaging of exemplar anti-inflammatory drugs enabled release of active molecules triggered by specific glycosidases of autochthonous gut bacteria. GlycoCaging ensured that drug efficacy was potentiated, and off-target effects were eliminated in murine models of inflammatory bowel disease. Biochemical and metagenomic analyses of gut microbiota of individual humans confirmed the broad applicability of this strategy.}, } @article {pmid40307949, year = {2025}, author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ}, title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {108}, pmid = {40307949}, issn = {2049-2618}, support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.}, } @article {pmid40307838, year = {2025}, author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C}, title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {170}, pmid = {40307838}, issn = {1466-609X}, support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; China ; Cross-Sectional Studies ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; *Health Personnel/statistics & numerical data ; Intensive Care Units/organization & administration/statistics & numerical data ; Prospective Studies ; }, abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?

DESIGN: Prospective, multicentre, cross-sectional study.

SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.

PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.

MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.

RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change = 1.22, 95% CI: 1.12-1.34, p < 0.001). The β-diversity of ARG between the two groups differed significantly (p = 0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall = 0.96, p for nonlinear = 0.84).

CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.

TRIAL REGISTRATION: NCT06228248.}, } @article {pmid40307239, year = {2025}, author = {Langwig, MV and Koester, F and Martin, C and Zhou, Z and Joye, SB and Reysenbach, AL and Anantharaman, K}, title = {Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4076}, pmid = {40307239}, issn = {2041-1723}, support = {DBI-2047598//National Science Foundation (NSF)/ ; OCE-2049478//National Science Foundation (NSF)/ ; }, mesh = {*Hydrothermal Vents/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; *Ecosystem ; Metagenome ; Genome, Viral ; Pacific Ocean ; Bacteriophages/genetics/classification ; Phylogeny ; Seawater/virology ; Gammaproteobacteria/virology ; Microbiota ; Virome ; }, abstract = {Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.}, } @article {pmid40307209, year = {2025}, author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B}, title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4048}, pmid = {40307209}, issn = {2041-1723}, support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; }, abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.}, } @article {pmid40306604, year = {2025}, author = {Lee, SH and Han, C and Shin, C}, title = {IUPHAR review: Microbiota-gut-brain axis and its role in neuropsychiatric disorders.}, journal = {Pharmacological research}, volume = {216}, number = {}, pages = {107749}, doi = {10.1016/j.phrs.2025.107749}, pmid = {40306604}, issn = {1096-1186}, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; *Brain/metabolism/microbiology ; *Mental Disorders/microbiology/therapy ; *Brain-Gut Axis ; Probiotics/therapeutic use ; Prebiotics ; }, abstract = {The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.}, } @article {pmid40305569, year = {2025}, author = {Hernandez-Valencia, JC and Gómez, GF and Correa, MM}, title = {Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320593}, pmid = {40305569}, issn = {1932-6203}, mesh = {Animals ; *Anopheles/virology ; Colombia ; *Virome/genetics ; *Metagenomics/methods ; *Mosquito Vectors/virology ; Phylogeny ; Malaria/transmission ; Metagenome ; }, abstract = {Anopheles darlingi is a main malaria vector in the neotropical region, but its viral component is not well studied, especially in the neotropics. This work aimed to analyze the virome in Anopheles darlingi from malaria endemic regions of Colombia. Specimens were collected from the Bajo Cauca, Chocoan Pacific and northwestern Amazonas regions and analyzed using an RNA-Seq approach. Results revealed a variety of RNA viral sequences with homology to those of Insect-Specific Viruses belonging to Rhabdoviridae, Partitiviridae, Metaviridae, Tymoviridae, Phasmaviridae, Totiviridae, Ortervirales and Riboviria. Despite geographical and ecological differences among regions, the An. darlingi viral composition remains consistent in different areas, with a core group of viral operational taxonomic units-vOTUs shared by the populations. Furthermore, diversity analysis uncovered greater dissimilarities in viral sequence among mosquitoes from geographically distant regions, particularly evident between populations located at both sides of the Andes Mountain range. This study provides the first characterization of the metavirome in An. darlingi from Colombia and lays the foundation for future research on the complex interactions among viruses, hosts, and microbiota; it also opens a new line of investigation on the viruses in Anopheles populations of Colombia.}, } @article {pmid40305442, year = {2025}, author = {Cayrou, C and Silver, K and Owen, L and Dunlop, J and Laird, K}, title = {Domestic laundering of healthcare textiles: Disinfection efficacy and risks of antibiotic resistance transmission.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321467}, pmid = {40305442}, issn = {1932-6203}, mesh = {*Disinfection/methods ; *Textiles/microbiology ; Humans ; *Laundering/methods ; Microbial Sensitivity Tests ; Detergents/pharmacology ; *Cross Infection/prevention & control/microbiology ; *Drug Resistance, Microbial ; Staphylococcus aureus/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; United Kingdom ; Microbiota/drug effects ; Decontamination/methods ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Enterococcus faecium/drug effects ; }, abstract = {Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are a major public health concern, with the evidence base for the potential role of textiles as fomites in microbial transmission growing. In the UK, domestic laundering machines (DLMs) are commonly used to clean healthcare worker uniforms, raising concerns about their effectiveness in microbial decontamination and role in AMR development. This study aimed to evaluate DLMs' ability to decontaminate microorganisms and their potential impact on AMR. The performance of six DLMs was assessed using Enterococcus faecium bioindicators under various wash cycles and detergent conditions. Shotgun metagenomics was used to analyse the microbiome and resistome of DLMs. The minimum inhibitory concentrations of domestic detergents were determined for Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, and detergent tolerance and antibiotic cross-resistance were assessed. Results showed only 50% (3/6) of DLMs achieved sufficient decontamination (≥5 log10 CFU reduction) at 60°C during full-length cycles, with rapid cycles performing inconsistently. Microbiome analysis revealed the presence of potentially pathogenic bacteria (e.g., Mycobacterium sp. Pseudomonas sp. and Acinetobacter sp.) and antibiotic resistance genes, including efflux pumps and target modification genes. Detergent tolerance assays showed increased bacterial tolerance to detergents, with cross-resistance to antibiotics observed in S. aureus and K. pneumoniae, including carbapenem and β-lactam groups. Whole genome sequencing identified mutations in genes encoding efflux pumps in S. aureus (MrgA) and K. pneumoniae (AcrB) after detergent exposure, which could impact efflux pump function. Findings suggest domestic laundering of healthcare uniforms may be insufficient for decontamination, posing risks for HAI transmission and AMR. Revising laundering guidelines to ensure effective DLM performance, detergent efficacy, and considering alternatives like onsite/industrial laundering are crucial to enhancing patient safety and controlling AMR in healthcare settings.}, } @article {pmid40304791, year = {2025}, author = {Bu, Y and Zhang, X and Xiong, Z and Li, K and Zhang, S and Lin, M and Zhao, G and Zheng, N and Wang, J and Zhao, S}, title = {Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {107}, pmid = {40304791}, issn = {1432-0614}, support = {2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202308//the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Fermentation/drug effects ; *Isoflavones/pharmacology/administration & dosage/metabolism ; *Trifolium/chemistry ; Genistein/pharmacology/administration & dosage ; *Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; Female ; Ammonia/metabolism ; Urease/metabolism ; Urea/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Metagenomics ; }, abstract = {Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH3-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.}, } @article {pmid40304704, year = {2025}, author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J}, title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.}, journal = {Molecular oral microbiology}, volume = {40}, number = {4}, pages = {137-146}, pmid = {40304704}, issn = {2041-1014}, support = {DE029612//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; R21 DE029612/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; DE028252//NIH-NIDCR/ ; }, mesh = {*Biofilms ; *In Situ Hybridization, Fluorescence/methods ; *Mouth/microbiology ; Humans ; Microbiota/genetics ; Streptococcus/genetics/classification ; Species Specificity ; *Bacteria/classification/genetics ; }, abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.}, } @article {pmid40304525, year = {2025}, author = {Fernández-Quintela, A and Laveriano-Santos, EP and Portolés, T and Gual-Grau, A and Sancho, JV and Portillo, MP}, title = {Changes in Liver Metabolome Induced by Pterostilbene and Resveratrol in a Rat Model of Liver Steatosis.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {15}, pages = {e70078}, pmid = {40304525}, issn = {1613-4133}, support = {AGL-2015-65719-R//Ministerio de Economía y Competitividad/ ; //Fondo Europeo de Desarrollo Regional (FEDER)/ ; CB12/03/30007//Instituto de Salud Carlos III (CIBERobn)/ ; IT1482-22//Government of the Basque Country/ ; }, mesh = {Animals ; *Stilbenes/pharmacology ; *Resveratrol/pharmacology ; Male ; *Liver/metabolism/drug effects ; *Metabolome/drug effects ; Gastrointestinal Microbiome/drug effects ; *Fatty Liver/metabolism/drug therapy ; Diet, High-Fat/adverse effects ; Rats ; Disease Models, Animal ; Rats, Sprague-Dawley ; Fructose/adverse effects ; }, abstract = {To gain more light on the effects of resveratrol and pterostilbene in the hepatic metabolic modifications in an in vivo model of diet-induced hepatic steatosis, and to explore their relationships with gut microbiota by untargeted metabolomics and metagenomics. Rats were divided into five groups receiving either a standard diet or a high-fat high-fructose (HFHF) diet supplemented or not with pterostilbene (15 or 30 mg/kg body weight/day; PT15 or PT30 groups, respectively) or resveratrol (30 mg/kg body weight/day; RSV30 group). Supplementation with the stilbenes reduced the hepatic steatosis induced by the HFHF diet. After the metabolomics study, 27 differentially expressed metabolites showed variable importance in projection scores > 1 and could be considered as potential biomarkers. Therefore, based on the pathway enrichment analysis, "riboflavin metabolism" and "nicotinate and nicotinamide metabolism" revealed significant enrichment. Further, riboflavin showed positive correlations to Eubacterium and Faecalibacterium, and negative correlations to Lactobacillus and Oscillospira genera. Nicotinamide mononucleotide was only positively correlated to the Ralstonia genus. The untargeted metabolomics approach showed that the actions of resveratrol or pterostilbene on the prevention of liver steatosis are mediated by specific mechanisms of action. Particularly, pterostilbene, but not resveratrol, is suggested to significantly enrich riboflavin or nicotinate and nicotinamide metabolic pathways.}, } @article {pmid40304520, year = {2025}, author = {Flörl, L and Meyer, A and Bokulich, NA}, title = {Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {5}, pages = {e0052425}, pmid = {40304520}, issn = {1098-5336}, support = {310030_204275//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 101060247//HORIZON EUROPE European Research Council/ ; 22.00210//Swiss State Secretariat for Education, Research, and Innovation/ ; //Swiss Government Excellence Scholarship/ ; }, mesh = {*Microbiota ; *Food Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Fermented Foods/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.}, } @article {pmid40302838, year = {2025}, author = {Pallen, MJ and Ponsero, AJ and Telatin, A and Moss, CJ and Baker, D and Heavens, D and Davidson, GL}, title = {Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.}, journal = {Access microbiology}, volume = {7}, number = {4}, pages = {}, pmid = {40302838}, issn = {2516-8290}, abstract = {Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.}, } @article {pmid40302016, year = {2025}, author = {Zhou, H and Tang, L and Fenton, KA and Song, X}, title = {Exploring and evaluating microbiome resilience in the gut.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40302016}, issn = {1574-6941}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Host Microbial Interactions ; Bacteria/genetics/classification ; Probiotics ; *Gastrointestinal Tract/microbiology ; Animals ; }, abstract = {The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.}, } @article {pmid40301729, year = {2025}, author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S}, title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {39}, pmid = {40301729}, issn = {2730-7182}, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.

RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200 m, with a slight increase observed above 1400 m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.

CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.}, } @article {pmid40301728, year = {2025}, author = {Munoz Briones, J and Brubaker, DK}, title = {A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {115}, pmid = {40301728}, issn = {1471-2105}, support = {R01 HD110367/HD/NICHD NIH HHS/United States ; 2120200//Directorate for Biological Sciences/ ; R01HD110367//National Institute of Child Health and Human Development/ ; }, mesh = {Humans ; *Microbiota ; *Metabolomics/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; *Computational Biology/methods ; Principal Component Analysis ; Crohn Disease/microbiology ; Multiomics ; }, abstract = {BACKGROUND: The number and size of multi-omics datasets with paired measurements of the host and microbiome is rapidly increasing with the advance of sequencing technologies. As it becomes routine to generate these datasets, computational methods to aid in their interpretation become increasingly important. Here, we present a framework for integration of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE integrates multi-omics data using single-omic latent variables (LV) organized in a structured meta-model to determine the combinations of features most predictive of a phenotype or condition.

RESULTS: We developed a supervised version of LIVE leveraging sparse Partial Least Squares Discriminant Analysis (sPLS-DA) LVs, and an unsupervised version leveraging sparse Principal Component Analysis (sPCA) principal components which both can incorporate covariate awarness. LIVE performance was tested on publicly available metagenomic and metabolomics data set from Crohn's Disease (CD) and Ulcerative Colitis (UC) status patients in the PRISM and LLDeep cohorts, and benchmarked against existing gut microbiome multi-omics approaches and vaginal microbiome datasests, achieving consistent and comparable performances. In addition to these benchmarking efforts, we present a detailed analysis and interpretation of both versions of LIVE using the PRISM and LLDeep cohorts. LIVE reduced the number of feature interactions from the original datasets for CD and UC from millions to less than 20,000 while conditioning the disease-predictive power of gut microbes, metabolites, enzymes, on clinical variables.

CONCLUSIONS: LIVE makes a distinct, complementary contribution to current methods to integrate microbiome data and offers key advantages to existing approaches in the interpretable integration of multi-omics data with clinical variables to predict to disease outcomes and identify microbiome mechanisms of disease.}, } @article {pmid40301726, year = {2025}, author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J}, title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {258}, pmid = {40301726}, issn = {1471-2180}, support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; }, mesh = {Humans ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Culture Media/chemistry ; *Biodiversity ; *Bacteriological Techniques/methods ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.}, } @article {pmid40300605, year = {2025}, author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH}, title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.}, journal = {Current biology : CB}, volume = {35}, number = {10}, pages = {2282-2294.e11}, doi = {10.1016/j.cub.2025.03.073}, pmid = {40300605}, issn = {1879-0445}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteriophages/physiology/genetics ; *Lysogeny ; Mice ; Animals ; *Bacteria/virology/genetics ; *Virome ; }, abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.}, } @article {pmid40298543, year = {2025}, author = {Bisaccia, M and Berini, F and Marinelli, F and Binda, E}, title = {Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40298543}, issn = {2079-6382}, support = {PNRA16_00105//Italian Ministry of Education, University and Research/ ; CMPT228810//Consorzio Interuniversitario per le Biotecnologie & Italian Ministry of Education, University and Research/ ; IBFM NBFC CN00000033//National Biodiversity Future Center/ ; PNRA22_0000040//Italian Ministry of Education, University and Research/ ; }, abstract = {The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.}, } @article {pmid40298412, year = {2025}, author = {Majernik, SN and Beaver, L and Bradley, PH}, title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.}, journal = {mSphere}, volume = {10}, number = {5}, pages = {e0085724}, pmid = {40298412}, issn = {2379-5042}, support = {R35 GM151155/GM/NIGMS NIH HHS/United States ; R35GM151155/NH/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Case-Control Studies ; Liver Cirrhosis/microbiology ; Genome, Bacterial ; }, abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.}, } @article {pmid40298386, year = {2025}, author = {Chen, Z and Zhang, Z and Nie, BN and Huang, W and Zhu, Y and Zhang, L and Xu, M and Wang, M and Yuan, C and Liu, N and Wang, X and Tian, J and Ba, Q and Wang, Z}, title = {Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0118824}, pmid = {40298386}, issn = {2379-5077}, support = {2022YQ066//Shanghai Municipal Health Commission/ ; 82304777//National Natural Science Foundation of China/ ; 23YF1442800//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; WL-HBQN-2021004K,WL-QNPY-2022004K//Shanghai Medical Innovation and Development Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Aging ; Aged ; *Colonic Neoplasms/microbiology ; Adult ; Feces/microbiology ; Metagenomics/methods ; Case-Control Studies ; Colorectal Neoplasms/microbiology ; }, abstract = {UNLABELLED: The human gut microbiome's role in colorectal cancer (CRC) pathogenesis has gained increasing recognition. This study aimed to delineate the microbiome characteristics that distinguish CRC patients from healthy individuals, while also evaluating the influence of aging, through a comprehensive metagenomic approach. The study analyzed a cohort of 80 CRC patients and 80 matched healthy controls, dividing participants into a normal and a CRC group, further categorized by age into young, middle-aged, and old-aged subgroups. Extensive metagenomic sequencing of fecal samples allowed for the exploration of both the structural and functional profiles of the microbiome, with findings validated in an independent cohort to ensure robustness. Our results highlight notable differences in microbiome composition between CRC patients and healthy individuals, which exhibit age-dependent variations. Specifically, a higher prevalence of pathogenic bacteria, such as Bacteroides vulgatus, known to drive inflammation and carcinogenesis, was observed in CRC patients, alongside a reduction in beneficial microbes, including Lactobacillus. Functionally, the CRC-associated microbiome showed an increase in pathways related to DNA repair, cell cycle regulation, and metabolic activities, such as the Citrate cycle and Galactose metabolism, underscoring distinct microbial alterations in CRC patients that could influence disease onset and progression. These insights lay a foundation for future research into microbiome-based diagnostics and treatments for CRC.

IMPORTANCE: This study underscores the critical role of the gut microbiome in colorectal cancer (CRC) pathogenesis, particularly in the context of aging. By identifying age-specific microbial biomarkers and functional pathways associated with CRC, our findings provide novel insights into how microbiome composition and metabolic activities influence disease progression. These discoveries pave the way for developing personalized microbiome-based diagnostic tools and therapeutic strategies, potentially improving CRC prevention and treatment outcomes across different age groups. Understanding these microbial dynamics could also inform interventions targeting gut microbiota to mitigate CRC risk and progression.}, } @article {pmid40298367, year = {2025}, author = {Zhou, Z and Ma, Y and Zhang, D and Ji, R and Wang, Y and Zhao, J and Ma, C and Zhu, H and Shen, H and Jiang, X and Niu, Y and Lu, J and Zhang, B and Tu, L and Zhang, H and Ma, X and Chen, P}, title = {Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0027625}, pmid = {40298367}, issn = {2379-5077}, support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27,2024-8-30,2024-4-2//The Lanzhou Municipal Science and Technology Program/ ; 20240260001,20240260017//The College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis/blood ; *Feces/microbiology ; Male ; Female ; *Metagenome/genetics ; Middle Aged ; *Dysbiosis/microbiology/diagnosis/blood ; *Cell-Free Nucleic Acids/blood ; Gastrointestinal Microbiome/genetics ; Adenoma/microbiology/diagnosis/blood ; Proof of Concept Study ; Aged ; Adult ; *Microbiota/genetics ; }, abstract = {Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.}, } @article {pmid40297591, year = {2025}, author = {Pei, X and Liu, L and Han, Y}, title = {Advances in human microbiome and prostate cancer research.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1576679}, pmid = {40297591}, issn = {1664-3224}, mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; }, abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.}, } @article {pmid40297587, year = {2025}, author = {Dora, D and Revisnyei, P and Pasic, A and Galffy, G and Dulka, E and Mihucz, A and Roskó, B and Szincsak, S and Iliuk, A and Weiss, GJ and Lohinai, Z}, title = {Host and bacterial urine proteomics might predict treatment outcomes for immunotherapy in advanced non-small cell lung cancer patients.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1543817}, pmid = {40297587}, issn = {1664-3224}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology ; Male ; Female ; *Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology ; Middle Aged ; *Proteomics/methods ; Aged ; Immunotherapy/methods ; Treatment Outcome ; *Proteome ; Biomarkers, Tumor/urine ; Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/therapeutic use ; }, abstract = {INTRODUCTION: Urine samples are non-invasive approaches to study potential circulating biomarkers from the host organism. Specific proteins cross the bloodstream through the intestinal barrier and may also derive from gut microbiota. In this study, we aimed to evaluate the predictive role of the host and bacterial urine extracellular vesicle (EV) proteomes in patients with non-small cell lung cancer (NSCLC) treated with anti-PD1 immunotherapy.

METHODS: We analyzed the urine EV proteome of 33 advanced-stage NSCLC patients treated with anti-PD1 immunotherapy with LC-MS/MS, stratifying patients according to long (>6 months) and short (≤6 months) progression-free survival (PFS). Gut microbial communities on a subcohort of 23 patients were also analyzed with shotgun metagenomics. Internal validation was performed using the Random Forest (RF) machine learning (ML) algorithm. RF was validated with a non-linear Bayesian ML model. Gene enrichment, and pathway analysis of host urine proteins were analyzed using the Reactome and Gene Ontology databases.

RESULTS: We identified human (n=3513), bacterial (n=2647), fungal (n=19), and viral (n=4) proteins. 186 human proteins showed differential abundance (p<0.05) according to PFS groups, 101 being significantly more abundant in patients with short PFS and n=85 in patients with long PFS. We found several pathways that were significantly enriched in patients with short PFS (vs long PFS). Multivariate Cox regression showed that human urine proteins MPP5, IGKV6-21, NT5E, and KRT27 were strongly associated with long PFS, and LMAN2, NUTF2, NID1, TNC, IGF1, BCR, GPHN, and PPBP showed the strongest association with short PFS. We revealed that an increased bacterial/host protein ratio in the urine is more frequent in patients with long PFS. Increased abundance of E. coli and E. faecalis proteins in the urine positively correlates with their gut metagenomic abundance. RF ML model supported the reliability in predicting PFS for critical human urine proteins (AUC=0.89), accuracy (95%) and Bacterial proteins (AUC=0.74).

CONCLUSION: To our knowledge, this is the first study to depict the predictive role of the host and bacterial urine proteome in anti-PD1-treated advanced NSCLC.}, } @article {pmid40297467, year = {2025}, author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D}, title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19120}, pmid = {40297467}, issn = {2167-8359}, mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.}, } @article {pmid40297464, year = {2025}, author = {Zhang, Y and Ding, G and Gao, Y and Li, Y and Zhou, P and Wu, L and Zhou, M and Wang, J and Tang, J}, title = {Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19384}, pmid = {40297464}, issn = {2167-8359}, mesh = {*Lakes/microbiology/chemistry ; China ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Chaohu Lake (CL) is one of the most polluted areas in China due to its high content of antibiotics. However, the distribution and influencing factors of antibiotic resistance genes (ARGs) in this lake are still controversial.

METHODS: To solve this problem, we used metagenomic sequencing to investigate the distribution and in-fluencing factors of ARGs in CL.

RESULTS: Our findings revealed the existence of nine kinds of ARGs, including 45 specific genes. The most abundant types were multidrug, bacitracin, polymyxin, macrolide lincosamide streptogramin, and aminoglycoside. Multiple microorganisms were undeniable ARG reservoirs, although they were not dominant species in the microbiota. Our results also showed that both the microbiota and physiochemical factors played important roles in shaping the distributions of ARGs in CL. Specifically, the levels of PO4-P (0.5927) and total phosphorus (0.4971) had a greater impact than total nitrogen (0.0515), NO3-N (0.0352), NO2-N (-0.1975), and NH3-N (-0.0952).

CONCLUSIONS: These findings provide valuable insights into the distribution and influencing factors of ARGs in lakes.}, } @article {pmid40296156, year = {2025}, author = {Fan, Y and Wang, D and Yang, JX and Ning, D and He, Z and Zhang, P and Rocha, AM and Xiao, N and Michael, JP and Walker, KF and Joyner, DC and Pan, C and Adams, MWW and Fields, MW and Alm, EJ and Stahl, DA and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {106}, pmid = {40296156}, issn = {2049-2618}, support = {DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; }, mesh = {*Groundwater/microbiology/chemistry ; Phylogeny ; *Microbiota/genetics ; Tennessee ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Nitrates/analysis ; Water Pollutants, Chemical/analysis ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; }, abstract = {BACKGROUND: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).

RESULTS: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.

CONCLUSIONS: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.}, } @article {pmid40295121, year = {2025}, author = {Scheffer, G and Rattray, J and Evans, P and Shi, W and Bhatnagar, S and Hubert, CRJ}, title = {Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40295121}, issn = {1574-6941}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //University of Calgary/ ; }, mesh = {*Nitrates/metabolism ; *Ponds/microbiology/chemistry ; *Oil and Gas Fields/microbiology ; Sulfates/metabolism ; *Bacteria/metabolism/genetics/classification ; *Water Microbiology ; Oxidation-Reduction ; Sulfides/metabolism ; Nitrites/metabolism ; Microbiota ; }, abstract = {Nitrate addition for mitigating sulfide production in oil field systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and reuse associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, and Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.}, } @article {pmid40294758, year = {2025}, author = {Thangadurai, T and Dobretsov, S and Aeby, G}, title = {Exploring bacterial diversity in Acropora pharaonis: Implications for coral health and growth anomalies.}, journal = {Microbial pathogenesis}, volume = {205}, number = {}, pages = {107616}, doi = {10.1016/j.micpath.2025.107616}, pmid = {40294758}, issn = {1096-1208}, mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; Phylogeny ; }, abstract = {Coral growth anomalies (GA) affect many coral genera across the world, yet the etiology of GAs remains unknown, with limited knowledge of associated bacteria. In this study, we investigated bacterial associations between the growth anomalies (GAs) and healthy (H) portions of coral colonies in Acropora faraonis for two seasons to understand microbial dynamics. Additionally, we examined bacteria in water (W), which could be affecting coral bacterial communities. We found that alpha diversity remained consistent between healthy and GA coral tissues, but their relative abundances differed significantly. Notably, differential analysis revealed the abundance of Endozoicomonas spp., differed significantly between GA and H tissue, although it remains the dominant genus in both GA and H tissue. The high relative abundance of Endozoicomonas spp. in both GA and healthy tissue underscores its potential role in maintaining coral health. Structural modifications in GAs, such as changes in polyp sizes or densities, could be responsible for these differences in bacterial abundance. Similarly, microbial community composition remained consistent between seasons but differed in abundance again. We found differences between microbial communities of GAs and water, but no significant differences were observed between GAs and H, and no previously established bacterial pathogens were detected in GA tissue. These findings describe bacterial community patterns in GAs, but their potential role in its pathogenesis remains unknown. Further metagenomic and meta-transcriptomic analyses are needed to understand potential bacterial involvement in GAs. Additionally, investigating viruses and fungi in GA tissue is recommended to gain deeper insights into GA pathogenesis.}, } @article {pmid40294554, year = {2025}, author = {Zeng, H and Yang, H and Fu, Z and Ma, L and Lu, L and Zeng, T and Xiao, Y and Lyu, W}, title = {Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota.}, journal = {Poultry science}, volume = {104}, number = {7}, pages = {105206}, pmid = {40294554}, issn = {1525-3171}, mesh = {Animals ; *Ducks/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Metagenomics ; *Bacteria/genetics/drug effects/isolation & purification ; *Drug Resistance, Microbial/genetics ; RNA, Bacterial/analysis ; }, abstract = {The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems.}, } @article {pmid40293591, year = {2025}, author = {Orlova, EA and Sinkov, VV and Ogarkov, OB and Suzdalnitsky, AE and Kondratov, IG and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI}, title = {Metagenomic Analysis of Caseum of Tuberculosis Foci.}, journal = {Bulletin of experimental biology and medicine}, volume = {178}, number = {5}, pages = {610-614}, pmid = {40293591}, issn = {1573-8221}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification/classification ; Metagenomics/methods ; *Tuberculoma/microbiology/pathology ; Male ; *Microbiota/genetics ; Lung/microbiology/pathology ; Female ; Middle Aged ; Adult ; Genome, Bacterial/genetics ; }, abstract = {The microbiota of the deep lung regions significantly differs from that of the upper respiratory tract by much lower biomass and dynamic diversity. In our previous studies we found that the biodiversity of the satellite microbiota of tuberculosis foci is sharply reduced in comparison with intact lung tissues. These findings allowed us to classify microbial communities in the caseous necrosis of tuberculomas into two types: (i) mycobacterial caseoma (tuberculoma), where 70% or more of the genomes correspond to Mycobacterium tuberculosis, and (ii) a polymicrobial community, where the concentration of M. tuberculosis varies from 0 to 10%. Using shotgun metagenomic sequencing, 14 tuberculomas from 13 patients were analyzed on a NextSeq 550 platform (Illumina). Taxonomic classification of short reads was performed using Kraken 2. The results show that, on average, 99.95% of the short reads belonged to human DNA or were unclassified. However, the classified reads related to bacterial genomes confirmed the concept that in many cases, tuberculomas contained polymicrobial communities that either replaced or supplemented the original mycobacterial microbiota of the caseous material.}, } @article {pmid40289251, year = {2025}, author = {Slager, J and Simpson, HL and Gacesa, R and Chen, L and Tan, IL and Gelderloos, J and Maatman, A and Wijmenga, C and Zhernakova, A and Fu, J and Weersma, RK and Gonera, G and Jonkers, IH and Withoff, S}, title = {High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2489071}, pmid = {40289251}, issn = {1949-0984}, mesh = {Humans ; *Celiac Disease/microbiology/diet therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Middle Aged ; Adult ; Netherlands ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Aged ; }, abstract = {BACKGROUND: Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterized by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution.

METHODS: To address these limitations, we analyzed fecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analyzed in tCeD patients and controls.

RESULTS: Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients.

CONCLUSION: Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome's role in intestinal health and disease.}, } @article {pmid40289152, year = {2025}, author = {Jarrige, D and Tardy, V and Loux, V and Rué, O and Chabbi, A and Terrat, S and Maron, PA}, title = {Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {14723}, pmid = {40289152}, issn = {2045-2322}, support = {ANR-20-PAMR-0004//Agence Nationale de la Recherche/ ; }, mesh = {*Soil Microbiology ; *Triticum ; *Metagenomics/methods ; *Microbiota/genetics ; *Grassland ; Bacteria/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; High-Throughput Nucleotide Sequencing ; }, abstract = {Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions. Metagenomics allows studying taxa that are often overlooked in microbiota studies, such as protists or viruses. Here, we employed metagenomics to characterise microbial successions after wheat straw input in a 4-month in-situ field study. We compared microbial successions patterns with those obtained by high throughput amplicon sequencing on the same soil samples to validate metagenomics as a tool for the fine analysis of microbial population dynamics in situ. Taxonomic patterns were concordant between the two methodologies but metagenomics allowed studying all the microbial groups simultaneously. Notably, our results evidenced that each domain displayed a specific dynamic pattern after wheat straw amendment. For instance, viral sequences multiplied in the early phase of straw decomposition, in parallel to copiotrophic bacteria, suggesting a "kill-the-winner" pattern that, to our knowledge, had not been observed before in soil. Altogether, our results highlighted that both inter and intra-domain trophic interactions were impacted by wheat amendment and these patterns depended on the land use history. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.}, } @article {pmid40289138, year = {2025}, author = {Weathers, SP and Li, X and Zhu, H and Damania, AV and Knafl, M and McKinley, B and Lin, H and Harrison, RA and Majd, NK and O'Brien, BJ and Penas-Prado, M and Loghin, M and Kamiya-Matsuoka, C and Yung, WKA and Solis Soto, LM and Maru, DM and Wistuba, I and Parra Cuentas, ER and Hernandez, S and Futreal, A and Wargo, JA and Schulze, K and Darbonne, WC and Ajami, NJ and Woodman, SE and de Groot, JF}, title = {Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3950}, pmid = {40289138}, issn = {2041-1723}, mesh = {Humans ; *Glioblastoma/genetics/immunology/mortality/therapy/drug therapy ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Female ; Middle Aged ; *Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy ; Temozolomide/therapeutic use/administration & dosage ; Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; Mutation ; Aged ; Adult ; *B7-H1 Antigen/antagonists & inhibitors ; Tumor Microenvironment ; Prospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use ; Treatment Outcome ; }, abstract = {This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.}, } @article {pmid40289100, year = {2025}, author = {Mok, K and Tomtong, P and Ogawa, T and Nagai, K and Torrungruang, P and Charoensiddhi, S and Nakayama, J and Wanikorn, B and Nitisinprasert, S and Vongsangnak, W and Nakphaichit, M}, title = {Synbiotic-driven modulation of the gut microbiota and metabolic functions related to obesity: insights from a human gastrointestinal model.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {250}, pmid = {40289100}, issn = {1471-2180}, support = {FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; }, mesh = {Humans ; *Synbiotics/administration & dosage ; *Obesity/microbiology/metabolism ; *Gastrointestinal Tract/microbiology/metabolism ; Feces/microbiology ; Limosilactobacillus reuteri/growth & development ; Bacteria/classification/genetics/isolation & purification/metabolism ; Microbial Viability ; Adult ; Male ; *Gastrointestinal Microbiome ; Female ; }, abstract = {Synbiotic interventions have gained increasing attention for modulating gut microbiota and metabolic functions in obesity-related disorders. This study evaluated the effects of Limosilactobacillus reuteri KUB-AC5 (10[8] CFU) and Wolffia globosa powder (6 g/day) using an in vitro continuous human gastrointestinal model. Fecal samples from obese donors were used to simulate the ascending and descending colon, with microbial viability, diversity, and metabolite production assessed over 14 days via culture-dependent and culture-independent methods. Synbiotic supplementation increased anaerobic bacterial counts by 2.6 log CFU/mL in the ascending colon and 2.2 log CFU/mL in the descending colon, with notable increases in lactic acid bacteria and reductions in Enterobacteriaceae. Metagenomic analysis revealed an increasing trend in microbial diversity and evenness after 7 days of treatment, though the changes were not statistically significant. PERMANOVA analysis confirmed significant shift in microbial community composition between stabilization, treatment, and washout periods (p < 0.05). Additionally, butyrate levels significantly increased (p < 0.05), while p-cresol, a deleterious metabolite, significantly decreased (p < 0.05). Bile acid composition was modulated, with increased tertiary bile acid 3-oxo-LCA and enhanced bile acid deconjugation, suggesting improved lipid metabolism and potential weight management benefits. These findings highlight the potential of synbiotic supplementation to enhance beneficial bacterial populations, improve microbial diversity, and support metabolic health in obesity management.}, } @article {pmid40289092, year = {2025}, author = {Qiu, J and Hu, P and Li, F and Huang, Y and Yang, Y and Sun, F and Wu, P and Lai, Y and Wang, Y and He, X and Dong, Y and Zhang, P and Zhang, S and Wu, N and Wang, T and Yang, S and Li, S and Yuan, J and Liu, X and Liu, G and Hu, Y and Wu, JHY and Chen, D and Pan, A and Pan, XF}, title = {Circulating linoleic acid and its interplay with gut microbiota during pregnancy for gestational diabetes mellitus.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {245}, pmid = {40289092}, issn = {1741-7015}, support = {2022YFC2702905//National Key R&D Program of China/ ; 82325043//the National Science Fund for Distinguished Young Scholars/ ; 82473646//Natural Science Foundation of China/ ; 2024NSFSC0578//Sichuan Provincial Natural Science Foundation/ ; YJ202346//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; Pregnancy ; Female ; *Diabetes, Gestational/blood/microbiology ; *Gastrointestinal Microbiome/physiology ; Adult ; Case-Control Studies ; *Linoleic Acid/blood ; China/epidemiology ; Mendelian Randomization Analysis ; }, abstract = {BACKGROUND: Circulating linoleic acid (LA) levels have been reported to be associated with various metabolic outcomes. However, the role of LA and its interplay with gut microbiota in gestational diabetes mellitus (GDM) remains unclear. This study aimed to investigate the longitudinal association between circulating LA levels during pregnancy and the risk of GDM, and the potential role of gut microbiota.

METHODS: A nested case-control study was conducted within the ongoing Tongji-Huaxi-Shuangliu Birth Cohort in Chengdu, China. Blood and fecal samples were collected during early and middle pregnancy from 807 participants. GDM was diagnosed in middle pregnancy using the International Association of Diabetes and Pregnancy Study Groups criteria. Plasma LA levels were measured using gas chromatography-mass spectrometry, and gut microbiota was analyzed through 16S rRNA gene sequencing and shotgun metagenomic sequencing. A two-sample Mendelian randomization study was conducted using data from the IEU OpenGWAS database and the FinnGen consortium.

RESULTS: Elevated plasma LA levels were associated with a lower risk of GDM in both early (P for trend = 0.002) and middle pregnancy (P for trend = 0.02). Consistently, Mendelian randomization analysis revealed that each unit increase in LA was associated with a 16% reduction in GDM risk (odds ratio: 0.84, 95% confidence interval: 0.72, 0.95). In early pregnancy, higher plasma LA levels were correlated with higher adiponectin levels (P < 0.001) and lower levels of triglycerides (P < 0.001), HbA1c (P = 0.04), and C-peptide (P = 0.04). The LA-accociated microbiota mediated the relationship between LA and C-peptide (P = 0.01). Additionally, the inverse association between LA and GDM was modified by Bilophila (P for interaction = 0.03), with a stronger association observed in participants with lower Bilophila levels in early pregnancy. Metagenomic analyses further showed that the LA-associated pathway (D-galacturonate degradation I) and its key enzyme (EC 4.2.1.7) were associated with metabolic traits.

CONCLUSIONS: Our study provides evidence for an inverse causal association between plasma LA levels during pregnancy and GDM risk, which is both mediated and modified by gut microbiota.}, } @article {pmid40288073, year = {2025}, author = {Song, Y and Baniakina, LFT and Jiang, L and Chai, L}, title = {Metagenomic insights into the alterations of gut microbial community in Bufo gargarizans tadpoles following lead exposure.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {55}, number = {}, pages = {101522}, doi = {10.1016/j.cbd.2025.101522}, pmid = {40288073}, issn = {1878-0407}, mesh = {Animals ; *Larva/microbiology/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; Metagenomics ; *Bufonidae/microbiology/growth & development ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of Bufo gargarizans tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 μg/L Pb group compared to the control group. Specifically, an increase in Bosea and Klebsiella was noted at 200 μg/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 μg/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 μg/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.}, } @article {pmid40287775, year = {2025}, author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W}, title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {105}, pmid = {40287775}, issn = {2049-2618}, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Glycine max/microbiology/growth & development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.}, } @article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, } @article {pmid40287117, year = {2025}, author = {Lu, W and Liu, Z and Song, Z and Wang, C and Yu, Z and Peng, S and Tian, Z and Lyu, A and Ning, Z}, title = {Vinegar-processed frankincense ameliorates ulcerative colitis by targeting BSH-active bacteria preference-mediated GDCA hydrolysis.}, journal = {Journal of ethnopharmacology}, volume = {348}, number = {}, pages = {119845}, doi = {10.1016/j.jep.2025.119845}, pmid = {40287117}, issn = {1872-7573}, mesh = {*Colitis, Ulcerative/drug therapy/chemically induced/microbiology ; Animals ; Mice ; *Acetic Acid/chemistry/pharmacology ; Hydrolysis ; Male ; *Amidohydrolases/metabolism ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Dextran Sulfate ; Mice, Inbred C57BL ; Bacteria/drug effects ; }, abstract = {Frankincense, is extensively used in both traditional Chinese medicine (TCM) and Indian practices for the treatment of ulcerative colitis (UC). In TCM, it is typically subjected to process with vinegar, which is believed to enhance its therapeutic efficacy. However, the underlying mechanism has yet to be elucidated.

AIM OF THE STUDY: To elucidate the underlying mechanism of frankincense vinegar processing from the perspective of bile salt hydrolase (BSH)-active bacteria preference and glycodeoxycholic acid (GDCA) hydrolysis.

MATERIALS AND METHODS: Dextran sodium sulfate (DSS)-induced UC model was used to elucidate the superior improving effects of vinegar-processed frankincense (PF). 16S rRNA and metagenomic sequencing along with ultra-high performance liquid chromatography-triple quadrupole mass spectroscopy (UHPLC-TQ-MS) were employed to reveal the differential bacteria and its related disturbance of GDCA. The effects of PF and GDCA on BSH-active bacteria were confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) and in vitro experiments. Finally, the pro-inflammatory effects of GDCA and the mechanisms by which PF ameliorates UC were verified by establishing a UC pseudo-sterile mice model with GDCA intervention.

RESULTS: PF exhibited remarkable mitigating effects on UC (P < 0.05 or P < 0.01). Specifically, PF enhanced the BSH activity of Bifidobacterium longum and Lactobacillus acidophilus (P < 0.01), thereby promoting their dissociation efficiency toward glycine-conjugated bile acids (G-CBAs), particularly GDCA (P < 0.01). Furthermore, PF reduced GDCA levels by regulating the dissociation efficiency of Bifidobacterium longum and Lactobacillus acidophilus toward GDCA, thereby alleviating GDCA-induced exacerbation of UC.

CONCLUSION: PF exhibits its superior amelioration effects on UC by enhancing the dissociation efficiency of Bifidobacteruum longum and Lactobacillus acidophilus towards G-CBAs, particularly GDCA.}, } @article {pmid40286059, year = {2025}, author = {Men, C and Pan, Z and Liu, J and Miao, S and Yuan, X and Zhang, Y and Yang, N and Cheng, S and Li, Z and Zuo, J}, title = {Single and Combined Effects of Aged Polyethylene Microplastics and Cadmium on Nitrogen Species in Stormwater Filtration Systems: Perspectives from Treatment Efficiency, Key Microbial Communities, and Nitrogen Cycling Functional Genes.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {7}, pages = {}, pmid = {40286059}, issn = {1420-3049}, support = {52400245//National Natural Science Foundation of China/ ; 2017ZX07103-007//National Key Research and Development Program of China/ ; 5221101156//National Natural Science Foundation of China/ ; }, mesh = {*Cadmium/chemistry ; *Microplastics/chemistry ; *Nitrogen Cycle/genetics/drug effects ; *Water Pollutants, Chemical ; *Nitrogen ; Filtration ; *Polyethylene/chemistry ; *Microbiota/drug effects ; Denitrification ; Water Purification/methods ; }, abstract = {Microplastics and heavy metal contamination frequently co-occur in stormwater filtration systems, where their interactions may potentially compromise nitrogen removal. Current research on microplastics and Cd contamination predominantly focuses on soils and constructed wetlands, with limited attention given to stormwater filtration systems. In this study, the single and synergistic effects of aged polyethylene microplastics (PE) and cadmium (Cd) contamination in stormwater infiltration systems were investigated from perspectives of nitrogen removal, microbial community structures, and predicted functional genes in nitrogen cycling. Results showed that PE single contamination demonstrated stronger inhibition on NO3[-]-N removal than Cd. Low-level PE contamination (PE content: 0.1% w/w) in Cd-contaminated systems showed stronger inhibitory effect than high-level PE contamination (PE content: 5% w/w). The mean NO3[-]-N removal efficiency under combined Cd50 (Cd concentration: 50 μg/L) and PE5 contamination during the sixth rainstorm event was 1.04 to 34.68 times that under other contamination scenarios. Metagenomic analysis identified keystone genera (Saccharimonadales, Enterobacter, Aeromonas, etc.), and critical nitrogen transformation pathways (nitrate reduction to ammonium, denitrification, nitrogen fixation, and nitrification) govern system performance. PE and Cd contamination effects were most pronounced on nitrification/denitrification enzymes beyond nitrite oxidase and nitrate reductase. These mechanistic findings advance our understanding of co-contaminant interactions in stormwater filtration systems.}, } @article {pmid40285962, year = {2025}, author = {Liao, J and Wei, JH and Liu, J and Ren, L and Zang, N and Liu, E}, title = {Respiratory virome in hospitalized children and analysis of its correlation with disease severity.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {7}, pages = {1643-1657}, pmid = {40285962}, issn = {1435-4373}, support = {Grant No. 82341111//The National Natural Science Foundation of China Special Project/ ; }, mesh = {Humans ; Male ; Female ; Child, Preschool ; Infant ; Child ; *Virome ; *Respiratory Tract Infections/virology/epidemiology ; Severity of Illness Index ; Bronchoalveolar Lavage Fluid/virology ; *Viruses/genetics/classification/isolation & purification ; Infant, Newborn ; Child, Hospitalized ; Sputum/virology ; High-Throughput Nucleotide Sequencing ; Adolescent ; *Virus Diseases/virology/epidemiology ; Metagenomics ; Hospitalization ; China/epidemiology ; }, abstract = {PURPOSE: To investigate the composition of respiratory viromes and their association with disease severity among hospitalized pediatric patients.

METHODS: Clinical data and metagenomic next-generation sequencing (mNGS) results were collected from pediatric patients hospitalized at the Children's Hospital of Chongqing Medical University between January 2022 and September 2023. The analyzed specimens included sputum and bronchoalveolar lavage fluid (BALF).

RESULTS: The study included 229 patients (65.07% male, median age 3 years) with 25 sputum and 204 BALF samples, of whom 40.17% met the WHO criteria for severe acute respiratory infection (SARI). Herpesviruses were detected in 166 cases (72.49%), including 85 cases of cytomegalovirus (CMV), 64 cases of Epstein-Barr virus (EBV), 34 cases of human herpesvirus-7 (HHV-7), 12 cases of human herpesvirus-6 (HHV-6), and 6 cases of herpes simplex virus type 1 (HSV-1). Additionally, 53 cases of torque teno virus (TTV) and 7 cases of torque teno mini virus (TLMV) were detected. CMV prevalence was highest in neonates, while EBV peaked in the 3-6 year group (37.78%). HSV-1 and HHV-6 were predominantly identified in severe infections.

CONCLUSION: Herpesviruses, particularly CMV and EBV, were the most frequently detected viruses, followed by anelloviruses. The age-specific viral distribution patterns provide novel epidemiological perspectives for understanding pediatric respiratory pathogenesis, though their clinical significance requires validation through mechanistic studies.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40285778, year = {2025}, author = {Alotaib, AS and Anwar, W and Albalawi, HQ and Albalawi, HS and Alshehri, MA and Al-Atawi, FM and Al Joundi, IT and Y Al Samini, A and Alqarni, RZ and Alzahrani, NE and Huraysi, MA}, title = {Metagenomic analysis microbial biodiversity of Trojena' the Mountains of Neom.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {4}, pages = {100-110}, doi = {10.14715/cmb/2025.71.4.13}, pmid = {40285778}, issn = {1165-158X}, mesh = {*Metagenomics/methods ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Saudi Arabia ; Soil Microbiology ; *Metagenome/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; }, abstract = {About 80% of the biosphere is constantly exposed to temperatures below 5 °C in cold environments. Microorganisms in cold environments can grow and decompose various organic compounds at sub-zero temperatures despite exposure to conditions that are harmful to their survival, such as sub-zero temperatures and low nutrient and water availability. The present study was designed to investigate metagenomic insights into the microbial diversity in (Al-Lawz Mountains / Trojena Mountains) Saudi Arabia. Metagenomic data sets are obtained by high-throughput sequencing of environmental soil samples and provide an aggregation of all the conceptually genetic materials of the intended area of this project. This study easily overcomes the bottlenecks associated with conventional molecular methods of retrieving genetic information and the unscientific shortage of microbial biodiversity research at Tabuk. High throughput bioinformatic analysis has been highlighted as the accurate exploration of the abundance and diversity of bacterial communities. Environmental DNA can be sequenced to identify the recent presence, relative abundance & distribution of a prokaryotic species or whole communities of bacteria. A total of 333 bacterial metagenomes were sequenced over two seasons, fall and winter. The 16S rRNA genes were quantified during this period. The most significant species regarding the relative abundance and diversity were in the location of sample1 by, Klebsiella michiganensis (251), stenotrophomonass maltophilia (110), Escherichia coli USML2 (88), Zhongshania aliphaticivorans (40), Acidibrevibacterium fodinaquatile (12) Calothrix spp. & Nibribacter ruber (10) Bacillus spp (10) respectively. On the other hand, the lowest abundances were in sample 4 location with Pseudomonas fluorescens (5) and Corynebacterium glutamicum (3) with (NA) species. This means these were unidentified yet. All these species have a growing demand for microbial biodiversity evaluations, given the pronounced impact of climate change in this region (Al-Lawz Mountains/Trojena Mountain). Benthic microbial communities are to be considered, given they have a potential role in CO2 and nitrogen fixation, which is related to plant growth-promoting properties. They can resist salinity, radiation, low-temperature adaptation, and biocontrol properties. Thus, eDNA cold-mountain biodiversity is a fraction of the time it costs to conduct conventional ecological monitoring.}, } @article {pmid40285533, year = {2025}, author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A}, title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70211}, doi = {10.1111/gcb.70211}, pmid = {40285533}, issn = {1365-2486}, support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; }, mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; }, abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.}, } @article {pmid40284601, year = {2025}, author = {Song, Z and Zhang, T and Liang, Y and Mcminn, A and Wang, M and Jiao, N and Luo, T}, title = {Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284601}, issn = {2076-2607}, abstract = {Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 Synechococcus cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of Synechococcus. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance Synechococcus strains underdetected by in situ samples. In addition, 24 clades representing Synechococcus subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of Synechococcus in the coastal waters of Xiamen. Furthermore, the Synechococcus community displayed pronounced seasonal variations, and temperature significantly influenced the variations in Synechococcus community composition. Additionally, Synechococcus populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of Synechococcus.}, } @article {pmid40284188, year = {2025}, author = {Bonomo, MG and D'Angelo, S and Picerno, V and Carriero, A and Salzano, G}, title = {Recent Advances in Gut Microbiota in Psoriatic Arthritis.}, journal = {Nutrients}, volume = {17}, number = {8}, pages = {}, pmid = {40284188}, issn = {2072-6643}, mesh = {Humans ; *Arthritis, Psoriatic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; }, abstract = {Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.}, } @article {pmid40283102, year = {2025}, author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD}, title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, pmid = {40283102}, issn = {2075-1729}, support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; }, abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.}, } @article {pmid40282295, year = {2025}, author = {Laguerre, H and Noël, C and Jégou, C and Fleury, Y and Le Chevalier, P}, title = {The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis.}, journal = {Biology}, volume = {14}, number = {4}, pages = {}, pmid = {40282295}, issn = {2079-7737}, abstract = {In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the same habitat in the Glénan Archipelago (Brittany, France) at different times for 2 years. The cœlomic microbiota were analyzed by targeted metagenomic with V4-16S metabarcoding and by a culturable approach with the isolation of strains and antimicrobial activity assays. Most of the OTUs of the cœlomic microbiota were affiliated with the phylum Proteobacteria and, notably, five orders: Burkholderiales, Flavobacteriales, Alteromonadales, Vibrionales and Pseudomonadales. Significant differences were observed regarding richness, biodiversity and composition between species and sampling dates. They could be explained by sub-abundant taxa that represented the global diversity. Cœlomic microbiota also revealed shared and unshared bacterial communities, validating a potential "specific" microbiota among the three Echinoderm species. Moreover, significant variations of the microbiota occurred among the sampling dates, suggesting a plasticity and, thus, a potential selection of these microbiota. Finally, out of the 831 bacterial strains isolated from culturable microbiota, 20 strains exhibited antibacterial activities, most of them assigned to the genera Shewanella, Pseudoalteromonas and Vibrio.}, } @article {pmid40280386, year = {2025}, author = {An, X and Zhao, R and Wang, L and Xiao, X and Xu, Z and Zhang, S and Xie, D and Xiao, Y and Zhang, Q}, title = {Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.}, journal = {Environmental research}, volume = {278}, number = {}, pages = {121688}, doi = {10.1016/j.envres.2025.121688}, pmid = {40280386}, issn = {1096-0953}, mesh = {*Thiocyanates/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; Metabolic Networks and Pathways ; *Water Pollutants, Chemical/metabolism ; *Bacteria/metabolism ; Thiobacillus/metabolism/genetics ; }, abstract = {Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated. Metagenomic analysis showed that Thiobacillus (77.73 %) were the primary degraders for the efficient degradation of thiocyanate. A total of 27 genes related to thiocyanate biodegradation were identified, including SCNase, COSase, sulfur oxidation, denitrification and carbon fixation. Metaproteomic revealed the high expression of chemotaxis protein and thioredoxin enhances cellular oxidative stress and maintains normal physiological metabolism. Additionally, the differentially expressed proteins were primarily involved in metabolic pathways including sphingolipid metabolism, energy metabolism, oxidative phosphorylation, two-component system and amino acid metabolism. Then the lipid, organic acid and amino acid metabolism were up-regulated by metabolomic analysis, thereby achieving the degradation of thiocyanate. Using a combination of qRT-PCR and parallel reaction monitoring (PRM), 27 key genes involved in thiocyanate biodegradation have been identified, providing a theoretical basis for developing microbial strategies to mitigate thiocyanate pollution. Molecular docking deepens the understanding of the interaction between degrading enzyme and thiocyanate. This study provides a theoretical basis for the microbial remediation of thiocyanate-containing wastewater.}, } @article {pmid40280272, year = {2025}, author = {Bačnik, K and Kranjc, L and Botella, L and Maguire, I and Pavić, D and Patoka, J and Dragičević, P and Bláha, M and Bielen, A and Kouba, A and Kutnjak, D and Hudina, S}, title = {Crayfish pet trade as a pathway for the introduction of known and novel viruses.}, journal = {Journal of invertebrate pathology}, volume = {211}, number = {}, pages = {108345}, doi = {10.1016/j.jip.2025.108345}, pmid = {40280272}, issn = {1096-0805}, mesh = {Animals ; *Astacoidea/virology ; *Introduced Species ; *Pets/virology ; *Virome ; }, abstract = {Expanding international pet trade has emerged as one of the main introduction pathways of aquatic invasive species, with ornamental crayfish species commonly available on the EU and global markets. Besides most frequently studied crayfish pathogens, such as Aphanomyces astaci and white spot syndrome virus (WSSV), ornamental crayfish carry associated microbial communities, which may potentially lead to the emergence of known or even novel diseases following intentional or unintentional release of animals into the wild. This is especially problematic in the case of viruses, which represent an important, yet considerably understudied, group of crayfish pathogens. Here we analyzed viromes of hepatopancreas tissue of four crayfish species acquired in the international pet trade in Europe (Procambarus clarkii, Procambarus alleni, Cherax holthuisi, and Cherax quadricarinatus) using a high throughput sequencing based metagenomic approach. Seven different known viruses were identified, which were previously either directly associated with crayfish (WSSV, Cherax quadricarinatus reovirus, chequa iflavirus, athtab bunya-like virus) or with hosts from subphylum Crustacea or invertebrates associated with freshwater environment (Shahe ispoda virus 5, Dicistroviridae sp.). Additional sequences represented 8 potential novel and divergent RNA viruses, most similar to sequences belonging to members of Picornavirales, Elliovirales, Reovirales, Hepelivirales, Tolivirales and Ghabrivirales orders. We discuss our findings in relation to their phylogenetic relationships, geographical origins, and putative pathogenicity implications. The results highlight the need for further research into the risks related to disease emergence associated with the pet trade.}, } @article {pmid40275408, year = {2025}, author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K}, title = {Unveiling plasmid diversity and functionality in pristine groundwater.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {42}, pmid = {40275408}, issn = {2524-6372}, abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.

CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.}, } @article {pmid40273394, year = {2025}, author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH}, title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.}, journal = {Neurology}, volume = {104}, number = {10}, pages = {e213592}, pmid = {40273394}, issn = {1526-632X}, mesh = {Humans ; *Caffeine/blood/metabolism ; *Parkinson Disease/blood/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Metabolomics ; Middle Aged ; Aged ; Coffee ; Cohort Studies ; Taiwan ; }, abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.

METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.

RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.

DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.}, } @article {pmid40272147, year = {2025}, author = {Dai, X and Cao, Y and Li, L and Gao, Y-X and Wang, J-X and Liu, Y-J and Ma, T-T and Zheng, J-M and Zhan, P-P and Shen, Z-Y}, title = {Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0162624}, pmid = {40272147}, issn = {2379-5077}, support = {82241219//National Natural Science Foundation of China/ ; 82127808//National Major Science and Technology Projects of China/ ; 81921004//National Natural Science Foundation of China/ ; NKTM2023005//Institute of Transplantation Medicine NanKai University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney Transplantation/adverse effects ; Female ; *Graft Rejection/metabolism/microbiology/diagnosis ; Male ; *Metabolome ; Adult ; Middle Aged ; Metabolomics/methods ; Feces/microbiology ; Multiomics ; }, abstract = {UNLABELLED: The gut microbiome and metabolome play crucial roles in renal allograft rejection progression. Integrated multiomics analyses may provide a comprehensive understanding of specific underlying mechanisms, which remain elusive. This study aimed to identify new approaches for clinical renal allograft rejection diagnosis and treatment. Thirty-five patients were divided into three groups: the rejection (n = 16), dysfunction (n = 7), and control (n = 12) groups. Metagenomic sequencing and nontargeted metabolomics were used to analyze stool and plasma samples. Significant microbiota, metabolites, and signaling pathways were identified. LASSO regression was used to construct a diagnostic model, and its diagnostic value was assessed via receiver operating characteristic curves. The microbiota composition and the related genes in the rejection group significantly differed from that in the dysfunction and control groups at the phylum, genus, and species levels (P < 0.001). The core species in the rejection group networks were Escherichia coli and Ruminococcus gnavus, while core species in the dysfunction group networks were Faecalibacterium prausnitzii and Bacteroides ovatus. The balance of specific microbial species was associated with kidney function in rejection patients. Spearman analysis revealed that specific differential species like Agathobaculum butyriciproducens and Gemmiger qucibialis were closely linked to the levels of serum 4-pyridoxic acid, 4-acetamidobutanoate, and fecal tryptamine from specific differential pathways. Finally, we constructed four clinical models to distinguish the rejection and dysfunction groups, and the model had excellent diagnostic performance. Altered gut microbiota may contribute to changes in metabolic pathway activity and metabolite abundance in rejection and dysfunction patients, which are strongly correlated with host immunological rejection. The diagnostic model, developed based on the gut microbiota and metabolites, has high clinical value for diagnosing renal rejection.

IMPORTANCE: This study aimed to screen new markers for non-invasive diagnosis by the gut microbiome and metabolome analysis, providing new insights into rejection mechanisms and identifying new approaches for clinical renal allograft rejection diagnosis.}, } @article {pmid40269516, year = {2025}, author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D}, title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40269516}, issn = {1477-4054}, support = {U24 CA231877/CA/NCI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; U24HG006620/NH/NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; }, abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.}, } @article {pmid40269515, year = {2025}, author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH}, title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40269515}, issn = {1477-4054}, support = {2430236//National Science Foundation/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; }, abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.}, } @article {pmid40269473, year = {2025}, author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL}, title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70088}, pmid = {40269473}, issn = {1758-2229}, support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; }, mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation & purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation & purification ; Machine Learning ; Brazil ; }, abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.}, } @article {pmid40269059, year = {2025}, author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M}, title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {14204}, pmid = {40269059}, issn = {2045-2322}, support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration & dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; }, abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.}, } @article {pmid40268958, year = {2025}, author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L}, title = {The dynamics of microbiome and virome in migratory birds of southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {64}, pmid = {40268958}, issn = {2055-5008}, mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; }, abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.}, } @article {pmid40267563, year = {2025}, author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T}, title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.}, journal = {Poultry science}, volume = {104}, number = {7}, pages = {105138}, pmid = {40267563}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Cecum/microbiology ; Metagenomics ; China ; *Genetic Variation ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; }, abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.}, } @article {pmid40263874, year = {2025}, author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y}, title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {208}, number = {}, pages = {116061}, doi = {10.1016/j.foodres.2025.116061}, pmid = {40263874}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; }, abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.}, } @article {pmid40263747, year = {2025}, author = {Liu, CG and Lin, MX and Xin, Y and Sun, M and Cui, J and Liu, D and Zang, D and Chen, J}, title = {Metagenomics and Non-Targeted Metabolomics Reveal the Role of Gut Microbiota and Its Metabolites in Brain Metastasis of Non-Small Cell Lung Cancer.}, journal = {Thoracic cancer}, volume = {16}, number = {8}, pages = {e70068}, pmid = {40263747}, issn = {1759-7714}, support = {2022RQ091//Science and Technology Talent Innovation Support Plan of Dalian/ ; 82203056//National Natural Science Foundation of China/ ; 2022LCYJYB01//The "1+X" program for Clinical Competency enhancement-Clinical Research Incubation Project of the Second Hospital of Dalian Medical University/ ; 2023-BS-167//Natural Science Foundation of Liaoning Province/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/secondary/metabolism ; *Lung Neoplasms/pathology/metabolism/microbiology ; *Metabolomics/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; Prognosis ; }, abstract = {BACKGROUND: Brain metastasis is a common and severe complication in non-small cell lung cancer (NSCLC) patients, significantly affecting prognosis. However, the role of gut microbiota and its metabolites in NSCLC brain metastasis remains poorly understood. This study aims to explore the relationship between gut microbiota, metabolites, and the development of brain metastasis in NSCLC.

METHODS: We conducted an integrative analysis combining metagenomics and non-targeted metabolomics on baseline fecal samples from NSCLC patients with brain metastasis (n = 18) and those without distant metastasis (n = 12). Gut microbiota composition and metabolite profiles were detected and analyzed, and statistical methods, including machine learning models, were applied to identify differences and potential biomarkers.

RESULTS: Significant differences in gut microbiota composition were found between the two groups, with higher microbial diversity observed in patients with brain metastasis. Specific genera, such as Paenibacillus, Fournierella, and Adlercreutzia, were enriched in the brain metastasis group. Metabolomic analysis revealed altered levels of short-chain fatty acids and other metabolites associated with immune modulation and vascular permeability, including angiotensin (1-7). These changes were linked to the metastatic process and may influence brain metastasis development. Furthermore, machine learning models identified key biomarkers, such as Raoultibacter, Mobilibacterium, and N-acetyl-L-glutamic acid, which could serve as valuable indicators for brain metastasis.

CONCLUSIONS: Our findings suggest that gut microbiota dysbiosis and its metabolic products may contribute to the development of brain metastasis in NSCLC. The identification of microbiota-derived biomarkers holds potential for early detection and therapeutic intervention in NSCLC brain metastasis.}, } @article {pmid40263287, year = {2025}, author = {Gao, D and Zhuang, Y and Liu, S and Ma, B and Xu, Y and Zhang, H and Nuermaimaiti, Y and Chen, T and Hou, G and Guo, W and You, J and Huang, Z and Xiao, J and Wang, W and Li, M and Li, S and Cao, Z}, title = {Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {61}, pmid = {40263287}, issn = {2055-5008}, support = {2024BBF01006//Key Research and Development Program of Ningxia/ ; 2023YFD1300904//National Key Research and Development Program of China/ ; 2024-KFKT-026//National Center of Technology Innovation for Dairy/ ; PC2023B02002//Pinduoduo-China Agricultural University Research Fund/ ; }, mesh = {Animals ; Cattle ; *Oxidative Stress ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Mice ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Metagenomics ; *Clostridiales/genetics/metabolism/isolation & purification ; Multiomics ; }, abstract = {An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10[8] cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.}, } @article {pmid40263159, year = {2025}, author = {Pandey, A and Israr, J and Pandey, J and Misra, S}, title = {Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {258}, pmid = {40263159}, issn = {1432-0991}, mesh = {*Biological Products/metabolism/pharmacology/isolation & purification/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/genetics ; Multigene Family ; Biosynthetic Pathways/genetics ; Microbiota ; }, abstract = {Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.}, } @article {pmid40262434, year = {2025}, author = {Lima, RAT and Garay, AV and Frederico, TD and de Oliveira, GM and Quirino, BF and Barbosa, JARG and Freitas, SM and Krüger, RH}, title = {Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome.}, journal = {Enzyme and microbial technology}, volume = {189}, number = {}, pages = {110654}, doi = {10.1016/j.enzmictec.2025.110654}, pmid = {40262434}, issn = {1879-0909}, mesh = {*Isoptera/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Glycoside Hydrolases/metabolism/chemistry/genetics ; Phylogeny ; *Bacterial Proteins/genetics/metabolism/chemistry ; Models, Molecular ; *Firmicutes/enzymology/genetics ; Substrate Specificity ; Enzyme Stability ; Hydrogen-Ion Concentration ; Amino Acid Sequence ; Temperature ; Kinetics ; }, abstract = {Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe[2 +]. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10[-5] μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.}, } @article {pmid40262432, year = {2025}, author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z}, title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.}, journal = {Water research}, volume = {282}, number = {}, pages = {123626}, doi = {10.1016/j.watres.2025.123626}, pmid = {40262432}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microbiota ; *Water Microbiology ; Temperature ; Drinking Water/microbiology ; Seasons ; }, abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.}, } @article {pmid40261064, year = {2025}, author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES}, title = {Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0156824}, pmid = {40261064}, issn = {2379-5077}, support = {R01 HD092311/HD/NICHD NIH HHS/United States ; 390237/CAPMC/CIHR/Canada ; BAA 75D30121C11084/CC/CDC HHS/United States ; 447944/CAPMC/CIHR/Canada ; R01HD092311/NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; *COVID-19/virology/epidemiology/microbiology/complications ; *HIV Infections/microbiology/virology/epidemiology/complications ; *Nasopharynx/microbiology/virology ; Kenya/epidemiology ; *SARS-CoV-2/genetics ; *Microbiota ; Longitudinal Studies ; Adult ; Child ; Male ; Child, Preschool ; Infant ; }, abstract = {UNLABELLED: The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome among individuals living with HIV is not fully characterized. Here, we describe the nasopharyngeal microbiome before, during, and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (P-values < 0.0001). In both mothers and children, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.

IMPORTANCE: The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.}, } @article {pmid40261045, year = {2025}, author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD}, title = {TEAL-Seq: targeted expression analysis sequencing.}, journal = {mSphere}, volume = {10}, number = {5}, pages = {e0098424}, pmid = {40261045}, issn = {2379-5042}, support = {F32 GM151856/GM/NIGMS NIH HHS/United States ; L70 AR084912/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; *Staphylococcus aureus/genetics ; *Microbiota/genetics ; *Staphylococcus epidermidis/genetics ; *Gene Expression Profiling/methods ; Metagenome ; Skin/microbiology ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; }, abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.}, } @article {pmid40260991, year = {2025}, author = {López-Gálvez, R and Orenes-Piñero, E and Rivera-Caravaca, JM and Pérez-Sanz, F and Ramos-Bratos, MP and Roca, MI and Mandaglio-Collados, D and López-García, C and Gil-Pérez, P and Esteve-Pastor, MA and Marín, F}, title = {Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {11}, pages = {e70046}, doi = {10.1002/mnfr.70046}, pmid = {40260991}, issn = {1613-4133}, support = {//Instituto de Salud Carlos III/ ; //Centro de investigación Biomédica en Red/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Acute Coronary Syndrome/microbiology/diet therapy/metabolism ; Male ; Female ; Middle Aged ; Dysbiosis/microbiology/diet therapy ; *Diet ; Aged ; Feces/microbiology ; Inflammation ; Case-Control Studies ; }, abstract = {Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.}, } @article {pmid40259731, year = {2025}, author = {Sun, YS and Zhao, L and Zheng, CL and Yan, XT and Li, Y and Gao, XL and Xue, TF and Zhang, YM and Li, ZP and Heller, R and Feng, CG and Xu, C and Wang, K and Qiu, Q}, title = {Convergent musk biosynthesis across host and microbiota in musk deer and muskrat.}, journal = {Zoological research}, volume = {46}, number = {3}, pages = {505-517}, doi = {10.24272/j.issn.2095-8137.2025.094}, pmid = {40259731}, issn = {2095-8137}, mesh = {Animals ; *Deer/microbiology/metabolism ; *Fatty Acids, Monounsaturated/metabolism ; *Microbiota ; Scent Glands/metabolism ; *Arvicolinae/microbiology/metabolism ; }, abstract = {Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.}, } @article {pmid40259344, year = {2025}, author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE}, title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {101}, pmid = {40259344}, issn = {2049-2618}, support = {R01 HL144651/HL/NHLBI NIH HHS/United States ; R01 HL148577/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation & purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation & purification ; Cecum/microbiology ; }, abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.}, } @article {pmid40258842, year = {2025}, author = {Duru, IC and Lecomte, A and Laine, P and Shishido, TK and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P}, title = {Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13723}, pmid = {40258842}, issn = {2045-2322}, support = {NNF22OC0080109//Novo Nordisk Foundation/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/isolation & purification ; Aged ; *Plasmids/genetics ; Male ; Female ; Middle Aged ; Feces/microbiology/virology ; Case-Control Studies ; Metagenomics/methods ; Machine Learning ; }, abstract = {The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.}, } @article {pmid40258509, year = {2025}, author = {Fang, C and Zhu, J and Xu, H and Qian, M and Jin, Y}, title = {Polystyrene microplastics and cypermethrin exposure interfered the complexity of antibiotic resistance genes and induced metabolic dysfunction in the gut of adult zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126288}, doi = {10.1016/j.envpol.2025.126288}, pmid = {40258509}, issn = {1873-6424}, mesh = {Animals ; *Zebrafish ; *Pyrethrins/toxicity ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polystyrenes/toxicity ; *Drug Resistance, Microbial/genetics ; Female ; }, abstract = {Environmental pollutants such as microplastics (MPs) and pesticides are becoming prevalent in aquatic ecosystems, posing risks to wildlife and human health. This study investigated the toxicological effects of polystyrene microplastics (PS-MPs) and cypermethrin (CYP) on adult female zebrafish (Danio rerio), focusing on intestinal microenvironment. Adsorption kinetics experimental results showed that PS-MPs can adsorb a certain amount of CYP on its surface, thereby forming a new type of composite pollutant. After exposure to red fluorescent PS-MPs for 4 days, it was found that the PS-MPs could enter the zebrafish and accumulate in the intestines. Five-month-old female zebrafish were exposed to PS-MPs, CYP, and a mixture of both for 21 days. After exposure, feces were collected and analyzed using metagenomic sequencing to determine microbial composition and functional changes. Metagenomic sequencing of naturally excreted feces showed that co-exposure synergistically reduced α-diversity and shifted community structure, with marked losses of beneficial Fusobacteriota, Firmicutes and Cetobacterium somerae and enrichment of pathogenic Preplasmiviricota. Functional annotation indicated that PS-MPs alone up-regulated glycoside hydrolases and glycosyl-transferases, whereas CYP and the co-exposure group suppressed a great number of the top 50 carbohydrate-active enzymes and decreased secondary metabolic pathways linked to amino-acid, lipid and carbohydrate metabolism pathways. Antibiotic-resistance gene (ARGs) profiling identified 57 ARG types (such as sul1, adeF, lnuC and mphA) after co-exposure. Finally, key genes related to amino acid metabolism, carbohydrate metabolism, and lipid metabolism in intestinal tissue were significantly altered. Collectively, our data demonstrated that PS-MPs and CYP exposure amplified gut dysbiosis, metabolic dysfunction and ARG complexity in zebrafish. Overall, the study highlighted the potential risks of combined environmental pollutants on intestinal microbiota, with implications for ecosystem health.}, } @article {pmid40255076, year = {2025}, author = {Buttler, L and Velázquez-Ramírez, DA and Tiede, A and Conradi, AM and Woltemate, S and Geffers, R and Bremer, B and Spielmann, V and Kahlhöfer, J and Kraft, ARM and Schlüter, D and Wedemeyer, H and Cornberg, M and Falk, C and Vital, M and Maasoumy, B}, title = {Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2487209}, pmid = {40255076}, issn = {1949-0984}, mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Dysbiosis/microbiology ; *Fungi/classification/isolation & purification/genetics ; *Inflammation/microbiology ; *Liver Cirrhosis/microbiology ; *Mycobiome ; Prospective Studies ; Metagenomics ; Intestinal Mucosa/microbiology ; *End Stage Liver Disease/microbiology/drug therapy ; Adult ; }, abstract = {Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation, and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were prospectively collected from 95 dLC-patients between 2017 and 2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing distinct microbial patterns. G1 (n = 39) displayed lowest diversity and highest Enterococcus abundance, G2 (n = 24) was dominated by Bifidobacteria, G3 (n = 29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed the lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp. (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n = 33; 86.8%), had highest plasma-levels of Zonulin (p = 0.044) and a proinflammatory cytokine profile along with numerically higher incidences of subsequent infections (p = 0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotic treatment significantly contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.}, } @article {pmid40254830, year = {2025}, author = {Pham, CM and Rankin, TJ and Stinear, TP and Walsh, CJ and Ryan, FJ}, title = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40254830}, issn = {1477-4054}, support = {GNT1194325//National Health and Medical Research Council of Australia/ ; }, mesh = {*Microbiota ; Humans ; *Software ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; }, abstract = {Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g. species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like gene set enrichment analysis are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, a taxon set enrichment analysis tool available as an R package, a web portal (https://shiny.taxsea.app), and a Python package. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) while also allowing users to incorporate custom sets such as taxonomic groupings. In silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from inflammatory bowel disease and type 2 diabetes metagenomic data, TaxSEA can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation, and advancing understanding of microbiome-host and environmental interactions.}, } @article {pmid40254251, year = {2025}, author = {Chang, FM and Chen, YH and Hsu, PS and Wu, TH and Sung, IH and Wu, MC and Nai, YS}, title = {RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.}, journal = {Journal of invertebrate pathology}, volume = {211}, number = {}, pages = {108341}, doi = {10.1016/j.jip.2025.108341}, pmid = {40254251}, issn = {1096-0805}, mesh = {Animals ; Bees/virology/parasitology ; *Varroidae/virology ; *Virome ; Metagenomics ; Taiwan ; *RNA Viruses/isolation & purification/genetics ; *Insect Viruses/genetics/isolation & purification ; }, abstract = {The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by an ecto-parasite that has spread worldwide, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.}, } @article {pmid40254113, year = {2025}, author = {Bartáková, V and Bryjová, A and Polačik, M and Alila, DO and Nagy, B and Watters, B and Bellstedt, D and Blažek, R and Žák, J and Reichard, M}, title = {Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure.}, journal = {Molecular phylogenetics and evolution}, volume = {208}, number = {}, pages = {108357}, doi = {10.1016/j.ympev.2025.108357}, pmid = {40254113}, issn = {1095-9513}, mesh = {Animals ; Tanzania ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Genetics, Population ; Genetic Variation ; Sequence Analysis, DNA ; Metagenomics ; Killifishes ; }, abstract = {Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.}, } @article {pmid40253770, year = {2025}, author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J}, title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.}, journal = {International immunopharmacology}, volume = {156}, number = {}, pages = {114645}, doi = {10.1016/j.intimp.2025.114645}, pmid = {40253770}, issn = {1878-1705}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Rats ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; *Diabetes Mellitus, Experimental/drug therapy/metabolism ; *Hypoglycemic Agents/pharmacology/therapeutic use ; Bile/metabolism ; Diet, High-Fat ; Glucagon-Like Peptide 1/metabolism ; Insulin Resistance ; Blood Glucose/metabolism ; Coptis chinensis ; }, abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.

PURPOSE: This study aims to investigate the effects of BPRC on the gut microbiota and its metabolite SCFAs in T2DM rats.

METHODS: T2DM rat model was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), followed by a 4-week treatment with BPRC to observe its therapeutic effects. The impact of BPRC on the gut microbiota was studied through metagenomic sequencing. Quantitative analysis of SCFAs was conducted using GC-MS. Western blot and quantitative real-time PCR (qRT-PCR) were conducted to investigate the potential mechanisms of BPRC.

RESULTS: BPRC significantly improved insulin resistance in T2DM rats, downregulated levels of pancreatic cell apoptosis factors, and upregulated the abundance of Bacteroides uniformis, Bacteroides sp A1C1, Anaerostipes caccae, Alistipes finegoldii and Blautia sp.N6H1-15 in T2DM rats. Additionally, BPRC increased the levels of seven SCFAs in the intestines of T2DM rats. It activated intestinal TGR5, GPR41, GPR43, and GPR109a receptors, collectively upregulating GLP-1 protein expression, and exerted therapeutic effects on T2DM.

CONCLUSION: The results indicate that the synergistic mechanism of BPRC in treating T2DM is associated with modulating the gut microbiota, increasing SCFAs content in the intestines, and regulating intestinal GLP-1 production.}, } @article {pmid40253169, year = {2025}, author = {Aryal, A and Nwachukwu, ID and Aryee, ANA}, title = {Examining the impact of crops and foods biofortified with micronutrients on the gut microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {209}, number = {}, pages = {116189}, doi = {10.1016/j.foodres.2025.116189}, pmid = {40253169}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/physiology ; *Micronutrients ; Humans ; *Crops, Agricultural ; *Biofortification ; *Food, Fortified ; Animals ; }, abstract = {Micronutrient deficiencies (MNDs) impact more than three billion individuals worldwide, particularly those in impoverished and marginalized communities, leading to adverse long-term health consequences. Biofortification, which focusses on enhancing the nutrient density of food crops, presents a promising strategy to address this challenge. Recent studies involving both model organisms and human subjects have demonstrated that, beyond remedying common dietary insufficiencies, micronutrients can modulate the composition and functionality of the gut microbiome. The microbiota, in turn, utilize these micronutrients, facilitating digestion, synthesizing essential nutrients, and modulating immune responses, thereby establishing a bidirectional relationship known as the micronutrient-microbiome axis. Numerous studies have also documented significant variations in these interactions, highlighting the complex dynamics of the micronutrient-microbiome relationship. The composition and interactions of the microbiota have been investigated using various methodologies, including 16S rRNA gene sequencing, RT-PCR, metagenomics, and metabolomics. This review explores recent advancements in understanding the reciprocal relationship between micronutrient levels and the gut microbiome, emphasizing key findings that provide critical insights for the development of targeted dietary strategies aimed at alleviating MNDs and improving overall health.}, } @article {pmid40252793, year = {2025}, author = {Yang, R and Guo, S and Huo, L and Yang, G and Tian, S}, title = {Impact of watershed-scale land restoration on soil microbial communities and their functions: Insights from metagenomic analysis.}, journal = {Environmental research}, volume = {277}, number = {}, pages = {121609}, doi = {10.1016/j.envres.2025.121609}, pmid = {40252793}, issn = {1096-0953}, mesh = {*Soil Microbiology ; China ; Metagenomics ; Phosphorus/metabolism ; Nitrogen/metabolism ; *Microbiota ; Soil/chemistry ; *Environmental Restoration and Remediation ; Carbon/metabolism ; Agriculture ; Biodiversity ; }, abstract = {Land restoration in the gully regions of China's Loess Plateau has significantly altered soil conditions and farming practices, yet its impact on soil microbes remains unclear. This study applied metagenomic sequencing and correlation analysis to examine microbial community shifts and key genes involved in carbon, nitrogen, and phosphorus cycling. Results show increased biodiversity and microbial activity, especially downstream, enhancing carbon metabolism and ecosystem resilience. Phosphorus activation improved, with related gene abundance rising by 27.45 %-52.57 %, facilitating phosphorus availability. Nitrogen cycling showed enhanced nitrification and nitrogen fixation, with reduced denitrification, promoting nitrogen retention. Soil organic carbon, total nitrogen, ammonium nitrogen, and available phosphorus (AP), particularly AP, strongly influenced microbial dynamics. These findings highlight the positive role of land restoration in improving soil health and nutrient cycling, supporting sustainable agriculture.}, } @article {pmid40252750, year = {2025}, author = {Yang, M and Peng, L and Mu, M and Yang, F and Li, Z and Han, B and Zhang, K}, title = {Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126277}, doi = {10.1016/j.envpol.2025.126277}, pmid = {40252750}, issn = {1873-6424}, mesh = {Animals ; *Oligochaeta ; *Manure/microbiology/analysis ; Metagenomics ; Livestock ; *Drug Resistance, Microbial/genetics ; Composting ; Anti-Bacterial Agents ; Metagenome ; Gastrointestinal Microbiome ; Bacteria/genetics ; }, abstract = {Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89 %) and Eisenia fetida (48.42 %), whereas Euryarchaeota (36.71 %) and Actinobacteria (39.42 %) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.}, } @article {pmid40252553, year = {2025}, author = {Bariod, L and Fuentes, E and Millet, M and White, J and Jacquiod, S and Moreau, J and Monceau, K}, title = {Exposure to pesticides is correlated with gut microbiota alterations in a farmland raptor.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109436}, doi = {10.1016/j.envint.2025.109436}, pmid = {40252553}, issn = {1873-6750}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Pesticides/toxicity ; Animals ; *Environmental Exposure ; Agriculture ; }, abstract = {The gut microbiota is crucial for host health and can be impacted by various environmental disruptions, yet the effects of multiple pesticide exposures on farmland organisms' microbiomes remain largely unexplored. We assessed microbiota changes in a wild apex predator exposed to multiple pesticides in agricultural landscapes. Pesticides, including acetochlor and quinoxyfen, which are supposed to be banned, were significantly positively correlated with certain key bacteria from Actinobacteria, Alphaproteobacteria and Gammaproteobacteria classes. Our results light up the potential collateral effect of pesticides on gut bacterial assemblages through unknown mechanisms. These effects could result in dysbiosis and the promotion of potential pathogens and/or the selection of bacteria that might allow the organism to detoxify the organism. Although formal metagenomic analyses would be required soon, these microbial shifts underline the broader ecological consequences of pesticide exposure, emphasising the need for integrated biodiversity conservation and ecosystem management to protect environmental and public health.}, } @article {pmid40252413, year = {2025}, author = {Okamura, T and Hasegawa, Y and Ohno, Y and Saijo, Y and Nakanishi, N and Honda, A and Hamaguchi, M and Takano, H and Fukui, M}, title = {Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet.}, journal = {Chemosphere}, volume = {379}, number = {}, pages = {144401}, doi = {10.1016/j.chemosphere.2025.144401}, pmid = {40252413}, issn = {1879-1298}, mesh = {Animals ; *Food Hypersensitivity/immunology ; *Diet, High-Fat/adverse effects ; Mice ; Mice, Inbred BALB C ; Gastrointestinal Microbiome/drug effects ; Ovalbumin/immunology ; Immunoglobulin E/blood ; *Microplastics/toxicity ; Administration, Oral ; *Polystyrenes/toxicity ; Female ; }, abstract = {The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.}, } @article {pmid40252307, year = {2025}, author = {Qian, L and Jiang, J and Zhang, Y and Huang, X and Che, Z and Chen, G and Liu, S}, title = {Sublethal exposure to boscalid induced respiratory abnormalities and gut microbiota dysbiosis in adult zebrafish.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {283}, number = {}, pages = {107370}, doi = {10.1016/j.aquatox.2025.107370}, pmid = {40252307}, issn = {1879-1514}, mesh = {Animals ; *Zebrafish/microbiology/physiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Dysbiosis/chemically induced/veterinary ; Gills/drug effects ; RNA, Ribosomal, 16S/genetics ; Bacteria/drug effects ; }, abstract = {Boscalid (BO), one of the frequently detected fungicides of succinate dehydrogenase inhibitor in water environments, has unknown effects on the respiratory function and gut health of aquatic organisms. Therefore, zebrafish were exposed to BO solutions (0.01-1.0 mg/L) for 21 days to assess its effects on zebrafish respiration and intestinal microbiota in this study. The results showed that exposure to 0.1 and 1.0 mg/L BO for 21 days resulted in zebrafish exhibiting aggregation of gill filaments, reduction of mucous cells, and significantly decreased opercular movement, linked to a marked decline in the activity of respiratory chain complex II. 16S rRNA gene sequencing revealed significant changes in the intestinal microbiota composition of zebrafish exposed to 1.0 mg/L BO. Specifically, the relative abundance of beneficial bacteria (Cetobacterium) was markedly reduced, while pathogenic bacteria (such as Ralstonia, Legionella, Acinetobacter, Escherichia/Shigella) associated with energy metabolism and immune pathways in zebrafish showed a significant increase in relative abundance. Accordingly, metagenomic functional prediction analysis further revealed the potential impact of BO-induced gut microbiota changes on energy metabolism and immune pathways in zebrafish. Furthermore, histopathological analysis of intestinal tissues revealed that exposure to BO resulted in necrosis and shedding of epithelial cells, as well as a decrease in goblet cell count, which exacerbated adverse effects on intestinal health. In conclusion, sublethal exposure to BO affects the respiratory function and intestinal health of zebrafish. Therefore, the impact of BO in aquatic environments on fish health warrants attention.}, } @article {pmid40252261, year = {2025}, author = {Li, B and Liang, C and Xu, B and Song, P and Liu, D and Zhang, J and Gu, H and Jiang, F and Gao, H and Cai, Z and Zhang, T}, title = {Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer.}, journal = {Microbiological research}, volume = {297}, number = {}, pages = {128182}, doi = {10.1016/j.micres.2025.128182}, pmid = {40252261}, issn = {1618-0623}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Deer/microbiology/metabolism ; *Seasons ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Tibet ; Feces/microbiology ; Metabolomics ; Phylogeny ; }, abstract = {Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.}, } @article {pmid40250281, year = {2025}, author = {Chen, Y and Hu, S and Hu, B and Li, Y and Chen, Z}, title = {Functional insights into microbial community dynamics and resilience in mycorrhizal associated constructed wetlands under pesticide stress.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138315}, doi = {10.1016/j.jhazmat.2025.138315}, pmid = {40250281}, issn = {1873-3336}, mesh = {*Wetlands ; *Mycorrhizae/drug effects/genetics/physiology ; *Pesticides/toxicity ; *Microbiota/drug effects ; Soil Microbiology ; Stress, Physiological ; Bacteria/genetics ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are critical mutualistic symbionts in most terrestrial ecosystems, where they facilitate nutrient acquisition, enhance plant resilience to environmental stressors, and shape the surrounding microbiome. However, its contributions (especially for microorganisms) to constructed wetlands (CWs) under pesticide stress remain poorly understood. This study investigated the effects of AMF on microbial community composition, diversity, metabolic pathways, and functional genes by metagenomics in CWs exposed to pesticides stress. Using comparative analyses of AMF-colonized and non-colonized CWs, we found that AMF enhanced overall microbial diversity, as evidenced by increases of 2.22 % (Chao1) and 2.83 % (observed species). Under fungicide stress, nitrogen-cycling microorganisms (e.g., Nitrososphaerota and Mucoromycota) increased in relative abundance, while carbon cycle-related microorganisms (e.g., Pseudomonadota and Bacteroidota) generally declined. AMF colonization improved microbial resilience, demonstrated by a 312 % rise in Rhizophagus abundance and significant increases in phosphorus-cycling microorganisms (e.g., Bradyrhizobium and Mesorhizobium). Functional gene analysis further revealed that AMF helped mitigate fungicide-induced reductions in genes related to nitrogen and carbon cycling, lowering the average decline rates to 4.02 % and 1.44 %, respectively, compared to higher rates in non-AMF treatments. In summary, these findings highlight the crucial role of AMF in enhancing pesticide stress resilience, maintaining microbial community stability, and improving the bioremediation capacity of CWs.}, } @article {pmid40250268, year = {2025}, author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC}, title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138285}, doi = {10.1016/j.jhazmat.2025.138285}, pmid = {40250268}, issn = {1873-3336}, mesh = {*Quorum Sensing ; Homeostasis ; *Ammonium Compounds/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; Nitrogen/metabolism ; 4-Butyrolactone/analogs & derivatives/pharmacology ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Anaerobiosis ; }, abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.}, } @article {pmid40250228, year = {2025}, author = {Wang, H and Yang, Q and Wang, S}, title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.}, journal = {The Science of the total environment}, volume = {978}, number = {}, pages = {179427}, doi = {10.1016/j.scitotenv.2025.179427}, pmid = {40250228}, issn = {1879-1026}, mesh = {*Triticum/growth & development ; *Soil Microbiology ; Soil/chemistry ; *Agriculture/methods ; Phosphorus/analysis ; Nitrogen/analysis ; Metagenomics ; Microbiota ; Carbon/analysis ; Nitrogen Cycle ; }, abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.}, } @article {pmid40250042, year = {2025}, author = {Menichini, D and De Seta, F and Mastrolia, SA and Cetin, I and Carafa, A and Santagni, S and Foschi, C and Cerboneschi, M and Smeazzetto, S and Neri, I and Facchinetti, F}, title = {Probiotics in pregnancy and group B streptococcus colonization: A multicentric, randomized, placebo-controlled, double-blind study with a focus on vaginal microbioma.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {310}, number = {}, pages = {113976}, doi = {10.1016/j.ejogrb.2025.113976}, pmid = {40250042}, issn = {1872-7654}, mesh = {Female ; Humans ; Pregnancy ; *Probiotics/therapeutic use/administration & dosage ; Double-Blind Method ; *Vagina/microbiology ; Adult ; *Streptococcus agalactiae ; *Streptococcal Infections/prevention & control/microbiology ; *Microbiota/drug effects ; *Pregnancy Complications, Infectious/microbiology ; Young Adult ; Pregnancy Trimester, Third ; }, abstract = {OBJECTIVE: To evaluate the feasibility and effects of the use of probiotics in pregnancy, starting in the third trimester, on rectovaginal colonization of group B streptococcus (GBS) in women at low obstetric risk.

METHODS: A multicentre, randomized, placebo-controlled, double-blind, parallel-group study was conducted in three tertiary hospitals in northern Italy and included low-risk pregnant women. The intervention consisted of oral administration of two capsules of probiotics or placebo from 30 weeks of pregnancy until 37 weeks of pregnancy. The primary outcome was GBS colonization, evaluated with rectovaginal swabs. In a subgroup, selected at random, changes in the vaginal microbiome after treatment administration were evaluated using 16S Metagenomic Sequencing Library Preparation sequencing and analysis.

RESULTS: In total, 267 pregnant women were randomized to receive probiotics (n = 133) or placebo (n = 134). The two groups were similar at baseline. After treatment, no differences were found in the rates of positive rectovaginal swabs (p = 0.24) and antibiotic administration (p = 0.27). Only one case of postpartum fever (>38 °C) was found in the placebo group. Labour and delivery outcomes and neonatal outcomes were similar in both groups. Analysis of the vaginal microbiota showed that the relative abundance of Lactobacillus spp. was not modified significantly by the probiotics, but the relative abundance of Gardnerella spp. decreased significantly (3.6 ± 7.9 vs 5.5 ± 10.2; p = 0.03). Interestingly, the relative abundance of Lactobacillus spp. reduced significantly in women who subsequently presented with partial rupture of membranes (46.9 ± 43.6 vs 77.7 ± 24.9; p = 0.02).

CONCLUSION: Although the clinical outcomes were unaffected, administration of probiotics led to favourable changes in vaginal microbiota. It remains to be established how this effect could be translated into clinical advantage.}, } @article {pmid40249033, year = {2025}, author = {Wei, Q and Chen, L and Yin, Y and Pai, M and Duan, H and Zeng, W and Hu, X and Xu, M and Li, S}, title = {Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70341}, doi = {10.1002/jmv.70341}, pmid = {40249033}, issn = {1096-9071}, support = {//This work was supported by the Chinese Society of Blood Transfusion Weigao Research Fund Project (CSBT-MWG-2020-02) and the Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Project (CAMS-2021-I2M-1-060)./ ; }, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *HIV Infections/microbiology/blood/drug therapy ; *Microbiota ; Metagenomics ; *Blood Donors ; *Bacteria/genetics/classification/isolation & purification ; Male ; Adult ; Female ; Middle Aged ; Sequence Analysis, DNA ; *Blood/microbiology ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.}, } @article {pmid40248366, year = {2025}, author = {Lu, X and Lu, Q and Zhu, R and Sun, M and Chen, H and Ge, Z and Jiang, Y and Wang, Z and Zhang, L and Zhang, W and Dai, Z}, title = {Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1582553}, pmid = {40248366}, issn = {2235-2988}, mesh = {Female ; Humans ; *Virome/genetics ; *Vagina/virology/microbiology ; *Metagenomics ; Phylogeny ; *Vaginitis/virology/microbiology ; Adult ; Microbiota ; Bacteriophages/genetics/classification ; *Viruses/classification/genetics/isolation & purification ; Middle Aged ; Biodiversity ; Young Adult ; Bacteria/classification/genetics ; }, abstract = {INTRODUCTION: The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.

METHODS: We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.

RESULTS: DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.

DISCUSSION: These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.}, } @article {pmid40247828, year = {2025}, author = {Doorenspleet, K and Mailli, AA and van der Hoorn, BB and Beentjes, KK and De Backer, A and Derycke, S and Murk, AJ and Reiss, H and Nijland, R}, title = {Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19158}, pmid = {40247828}, issn = {2167-8359}, mesh = {*Biodiversity ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; North Sea ; Nanopores ; Belgium ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.}, } @article {pmid40247632, year = {2025}, author = {Lee, JS and Kao, DJ and Worledge, CS and Villamaria, ZF and Wang, RX and Welch, NM and Kostelecky, RE and Colgan, SP}, title = {E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2490211}, pmid = {40247632}, issn = {1949-0984}, support = {K01 DK129410/DK/NIDDK NIH HHS/United States ; K08 DK120809/DK/NIDDK NIH HHS/United States ; IK6 BX006475/BX/BLRD VA/United States ; R01 DK050189/DK/NIDDK NIH HHS/United States ; R01 DK131581/DK/NIDDK NIH HHS/United States ; I01 BX002182/BX/BLRD VA/United States ; R37 DK050189/DK/NIDDK NIH HHS/United States ; R01 DK095491/DK/NIDDK NIH HHS/United States ; R01 DK104713/DK/NIDDK NIH HHS/United States ; L30 DK133994/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Wound Healing ; Gastrointestinal Microbiome ; Mice ; *Purines/metabolism ; *Colon/microbiology/metabolism/pathology ; *Butyrates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Colitis/chemically induced/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Male ; }, abstract = {The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.}, } @article {pmid40246602, year = {2025}, author = {Zeng, S and Wang, S and Mu, D}, title = {Metagenomics for IgA-coated gut microbiota: from taxonomy to function.}, journal = {Trends in microbiology}, volume = {33}, number = {8}, pages = {823-825}, doi = {10.1016/j.tim.2025.04.001}, pmid = {40246602}, issn = {1878-4380}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Immunoglobulin A/immunology/metabolism/genetics ; *Bacteria/genetics/classification ; }, abstract = {Immunoglobulin A (IgA) establishes intricate interactions with human gut microbiota, thereby forming IgA-coated microbiota. This forum first explores state-of-the-art metagenomic techniques for characterizing IgA-coated microbiota. Thereafter, metagenomic insights into its taxonomic diversity and microbial genomic functions that mediate IgA coating are provided. Finally, clinical implications for human health are highlighted.}, } @article {pmid40246210, year = {2025}, author = {Wani, AK and Qadir, F and Elboughdiri, N and Rahayu, F and Saefudin, and Pranowo, D and Martasari, C and Kosmiatin, M and Suhara, C and Sudaryono, T and Prayogo, Y and Yadav, KK and Muzammil, K and Eltayeb, LB and Alreshidi, MA and Singh, R}, title = {Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.}, journal = {Biotechnology advances}, volume = {82}, number = {}, pages = {108580}, doi = {10.1016/j.biotechadv.2025.108580}, pmid = {40246210}, issn = {1873-1899}, mesh = {*Symbiosis ; *Soil Microbiology ; *Metagenomics/methods ; Nitrogen/metabolism ; Phosphorus/metabolism ; *Plants/microbiology/metabolism ; Sulfur/metabolism ; *Microbiota ; *Carbon Sequestration ; Soil/chemistry ; Carbon/metabolism ; }, abstract = {Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.}, } @article {pmid40245686, year = {2025}, author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, Á and Muñoz, S and García-Cañas, V}, title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {262}, number = {}, pages = {116896}, doi = {10.1016/j.jpba.2025.116896}, pmid = {40245686}, issn = {1873-264X}, mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; *Methylamines/metabolism ; Metabolomics/methods ; *Fatty Acids, Volatile/metabolism ; Humans ; *Digestion/physiology ; *Nanopore Sequencing/methods ; Plant Extracts/pharmacology ; Models, Biological ; Fermentation ; Transcriptome ; }, abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.}, } @article {pmid40244481, year = {2025}, author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R}, title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {248}, pmid = {40244481}, issn = {1432-0991}, support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; }, mesh = {Thailand ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; }, abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.}, } @article {pmid40244477, year = {2025}, author = {Li, J and Zhang, Y and He, L}, title = {The role of urine microbiota in culture-negative patients with pyuria.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {227}, pmid = {40244477}, issn = {1433-8726}, mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; }, abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.

METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.

RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p = 0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p = 0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p = 0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p = 0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p < 0.001].

CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.}, } @article {pmid40244062, year = {2025}, author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC}, title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40244062}, issn = {1751-7370}, support = {COEVOPRO 802242//European Research Council Starting/ ; 802242//European Research Council Starting Grant/ ; //EPA Cephalosporin Junior Research Fellowship at Linacre College/ ; }, mesh = {Animals ; *Evolution, Molecular ; *Dysbiosis/microbiology ; *Microbiota ; *Staphylococcus aureus/genetics/pathogenicity/physiology ; Virulence ; Whole Genome Sequencing ; *Host-Pathogen Interactions ; Biofilms/growth & development ; Caenorhabditis elegans/microbiology ; }, abstract = {Pathogens newly invading a host must compete with resident microbiota. This within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a natural microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.}, } @article {pmid40243577, year = {2025}, author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J}, title = {Potential Role of Malassezia restricta in Pterygium Development.}, journal = {International journal of molecular sciences}, volume = {26}, number = {7}, pages = {}, pmid = {40243577}, issn = {1422-0067}, support = {IP-2020-02-8921//Croatian Science Foundation/ ; }, mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; }, abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.}, } @article {pmid40240641, year = {2025}, author = {Muñoz-Rivera, MP and Martínez-Morales, F and Morales-Guzmán, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR}, title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40240641}, issn = {1618-1905}, abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.}, } @article {pmid40240456, year = {2025}, author = {Bahetjan, K and Yu-Xia, and Lin, S and Aili, N and Yang, H and Du, S}, title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13179}, pmid = {40240456}, issn = {2045-2322}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; }, abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.}, } @article {pmid40240384, year = {2025}, author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, JÉCT and Arruda, P and Dante, RA and Gerhardt, IR}, title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {636}, pmid = {40240384}, issn = {2052-4463}, support = {2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; }, mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.}, } @article {pmid40239498, year = {2025}, author = {Chen, M and Grégoire, DS and St-Germain, P and Berdugo-Clavijo, C and Hug, LA}, title = {Microbial diversity and capacity for arsenic biogeochemical cycling in aquifers associated with thermal mobilization.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179357}, doi = {10.1016/j.scitotenv.2025.179357}, pmid = {40239498}, issn = {1879-1026}, mesh = {*Arsenic/analysis/metabolism ; *Groundwater/microbiology/chemistry ; *Water Pollutants, Chemical/analysis/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Alberta ; Bacteria/metabolism ; Biodegradation, Environmental ; }, abstract = {Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic detoxification and metabolism, which include genes for efflux, methylation, and reduction/oxidation of As(V)/As(III). We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread among community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high‑arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.}, } @article {pmid40238917, year = {2025}, author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ}, title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.}, journal = {Science translational medicine}, volume = {17}, number = {794}, pages = {eadq8870}, pmid = {40238917}, issn = {1946-6242}, support = {F30 CA257378/CA/NCI NIH HHS/United States ; R01 CA255116/CA/NCI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Bacteria/genetics/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; *Operon/genetics ; *Pyrimidines/toxicity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.}, } @article {pmid40238748, year = {2025}, author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C}, title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321389}, pmid = {40238748}, issn = {1932-6203}, mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; }, abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.}, } @article {pmid40238740, year = {2025}, author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X}, title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013069}, pmid = {40238740}, issn = {1553-7374}, mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; }, abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.}, } @article {pmid40237492, year = {2025}, author = {Hu, T and Meng, Y and Zhao, C and Sheng, D and Yang, S and Dai, J and Wei, T and Zhang, Y and Zhao, G and Liu, Y and Wang, Q and Zhang, L}, title = {Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.}, journal = {Microbiology spectrum}, volume = {13}, number = {6}, pages = {e0298424}, pmid = {40237492}, issn = {2165-0497}, mesh = {*Candida albicans/growth & development/drug effects/metabolism ; Female ; Humans ; *Vagina/microbiology ; *Lactobacillus/metabolism/genetics/classification ; Candidiasis, Vulvovaginal/microbiology ; Microbiota ; Antibiosis ; Adult ; Microbial Interactions ; Metagenomics ; }, abstract = {As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.}, } @article {pmid40237489, year = {2025}, author = {Rybicka, I and Kaźmierczak, Z}, title = {The human phageome: niche-specific distribution of bacteriophages and their clinical implications.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {6}, pages = {e0178824}, pmid = {40237489}, issn = {1098-5336}, support = {UMO-2019/35/B/NZ7/01824//Narodowe Centrum Nauki/ ; UMO-2023/51/D/NZ7/02145//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; *Bacteriophages/physiology/genetics/isolation & purification ; *Bacteria/virology ; *Virome ; *Microbiota ; Gastrointestinal Microbiome ; }, abstract = {Bacteriophages (phages) play a crucial role in shaping the composition and diversity of the human microbiome across various body niches. Recent advancements in high-throughput sequencing technologies have enabled comprehensive analysis of the human phageome in different body sites. This review comprehensively analyzes phage populations across major human body niches, examining their distribution and dynamics through recent metagenomic discoveries. We explore how phage-bacteria interactions within different body sites contribute to homeostasis and disease development. Emerging evidence demonstrates that phageome perturbations can serve as early indicators of various disorders, particularly in the gut microbiome. Understanding these complex microbial interactions offers promising opportunities for developing novel diagnostic markers and therapeutic approaches. However, the causal relationship between phages, bacteria, and disease development remains unclear. Further research is needed to elucidate the role of phages in human health and disease and to explore their potential as diagnostic or therapeutic tools. Understanding the intricate interactions between phages, bacteria, and the human host is crucial for unraveling the complexities of the human microbiome and its impact on health and disease.}, } @article {pmid40237336, year = {2025}, author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR}, title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2493900}, pmid = {40237336}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; }, abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.}, } @article {pmid40234093, year = {2025}, author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ}, title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {4}, pages = {}, pmid = {40234093}, issn = {2051-1426}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Azetidines/therapeutic use/pharmacology ; Gastrointestinal Microbiome ; *Melanoma/drug therapy/pathology/mortality ; *Neoadjuvant Therapy/methods ; Neoplasm Staging ; *Piperidines/pharmacology/therapeutic use ; *Skin Neoplasms/drug therapy ; Treatment Outcome ; *Vemurafenib/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

TRIAL REGISTRATION NUMBER: NCT03554083.}, } @article {pmid40233938, year = {2025}, author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM}, title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, pmid = {40233938}, issn = {1365-2672}, support = {R01 MH125246/MH/NIMH NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; }, mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation & purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; }, abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.

METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.

CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.}, } @article {pmid40233768, year = {2025}, author = {Tinker, KA and Anthony, W and Brandi, M and Flett, S and Bagwell, CE and Smallwood, C and Davis, R and Gulliver, D}, title = {Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70076}, pmid = {40233768}, issn = {1758-2229}, support = {//U.S. Department of Energy's (DOE) Office of Fossil Energy and Carbon Management's Hydrogen with Carbon Management Program and executed through the National Energy Technology Laboratory (NETL) Research & Innovation Center's Natural Gas Decarbonization and Hydrogen Technologies Multi-Year Research Plan/ ; }, mesh = {*Hydrogen/metabolism ; *Groundwater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Illinois ; Methane/metabolism ; Microbiota ; Metagenomics ; }, abstract = {Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.}, } @article {pmid40233040, year = {2025}, author = {Pomej, K and Frick, A and Scheiner, B and Balcar, L and Pajancic, L and Klotz, A and Kreuter, A and Lampichler, K and Regnat, K and Zinober, K and Trauner, M and Tamandl, D and Gasche, C and Pinter, M}, title = {Study protocol: Fecal Microbiota Transplant combined with Atezolizumab/Bevacizumab in Patients with Hepatocellular Carcinoma who failed to achieve or maintain objective response to Atezolizumab/Bevacizumab - the FAB-HCC pilot study.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321189}, pmid = {40233040}, issn = {1932-6203}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Bevacizumab/therapeutic use/administration & dosage ; *Carcinoma, Hepatocellular/therapy/drug therapy ; *Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome ; *Liver Neoplasms/therapy/drug therapy ; Pilot Projects ; Clinical Trials, Phase II as Topic ; }, abstract = {BACKGROUND: The gut microbiota is often altered in chronic liver diseases and hepatocellular carcinoma (HCC), and increasing evidence suggests that it may influence response to cancer immunotherapy. Strategies to modulate the gut microbiome (i.e., fecal microbiota transplant (FMT)) may help to improve efficacy of immune checkpoint inhibitors (ICIs) or even overcome resistance to ICIs. Here, we describe the design and rationale of FAB-HCC, a single-center, single-arm, phase II pilot study to assess safety, feasibility, and efficacy of FMT from patients with HCC who responded to PD-(L)1-based immunotherapy or from healthy donors to patients with HCC who failed to achieve or maintain a response to atezolizumab plus bevacizumab.

METHODS: In this single-center, single-arm, phase II pilot study (ClinicalTrials.gov identifier: NCT05750030), we plan to include 12 patients with advanced HCC who failed to achieve or maintain a response to atezolizumab/bevacizumab. Patients will receive a single FMT via colonoscopy from donors with HCC who responded to PD-(L)1-based immunotherapy or from healthy individuals, followed by atezolizumab/bevacizumab every 3 weeks. The primary endpoint is safety, measured by incidence and severity of treatment-related adverse events. The main secondary endpoint is efficacy, as assessed by best radiological response according to RECISTv1.1 and mRECIST. Additional exploratory endpoints include data on the effect of FMT on recipient gut microbiota, as well as metagenomic analysis of stool samples, analyses of circulating immune cells and serum and stool proteomic, metabolomic and lipidomic signatures.

DISCUSSION: The results of this study will help to define the potential of FMT as add-on intervention in the systemic treatment of advanced HCC, with the potential to improve efficacy of immunotherapy or even overcome resistance.

TRIAL REGISTRATION: EudraCT Number: 2022-000234-42 Clinical trial registry & ID: ClinicalTrials.gov identifier: NCT05750030 (Registration date: 16.01.2023).}, } @article {pmid40232948, year = {2025}, author = {Leech, SM and Barrett, HL and Dorey, ES and Mullins, T and Laurie, J and Nitert, MD}, title = {Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, pmid = {40232948}, issn = {2057-5858}, mesh = {Humans ; Female ; Pregnancy ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/genetics ; Adult ; *Diabetes, Gestational/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.}, } @article {pmid40230307, year = {2025}, author = {Liu, B and He, N and Li, H and Yang, Z and Lin, Y and Wu, X and Zhang, H and Zhang, Z and Zhang, Z and Tian, Y and Wu, Z and Zou, Y and Peng, J and Li, S}, title = {3-Fucosyllactose Prevents Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota-Derived Pantothenate in Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {16}, pages = {9637-9649}, doi = {10.1021/acs.jafc.5c00079}, pmid = {40230307}, issn = {1520-5118}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Pantothenic Acid/metabolism ; *Non-alcoholic Fatty Liver Disease/metabolism/microbiology/prevention & control/drug therapy ; Male ; Mice, Inbred C57BL ; Humans ; Diet, High-Fat/adverse effects ; Liver/metabolism ; *Trisaccharides/administration & dosage ; Prebiotics/administration & dosage/analysis ; Lipid Metabolism/drug effects ; Bacteria/isolation & purification/classification/genetics/metabolism ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health threat. Human milk oligosaccharides (HMOs) exhibit prebiotic properties that may alleviate NAFLD progression. Herein, our study demonstrates that 3-fucosyllactose (3-FL), a distinctive and crucial HMO, significantly attenuates body weight gain, enhances hepatic lipid metabolism, and reduces inflammation in a high-fat diet (HFD)-induced NAFLD mouse model. These findings suggest its potential as a dietary supplement for preventing and alleviating NAFLD progression. Subsequently, fecal metagenomic and nontargeted metabolomics analyses revealed that 3-FL treatment significantly alleviated HFD-induced gut microbiota dysbiosis, with a specific enhancement of the pantothenate (vitamin B5) metabolic pathways. Our targeted metabolite analysis further revealed a significant increase in both hepatic and fecal pantothenate concentrations, which contributed to the enhancement of the coenzyme A (CoA)-mediated lipid metabolism pathway. Furthermore, the subsequent population cohort analyses revealed a significant correlation between serum pantothenate levels and the progression of NAFLD, thereby reinforcing its candidacy as a noninvasive diagnostic biomarker. These findings show that 3-FL acts as an effective prebiotic to alleviate NAFLD symptoms, in part by enhancing the gut microbiota-mediated pantothenate/CoA metabolic pathway.}, } @article {pmid40229213, year = {2025}, author = {Hoops, SL and Moutsoglou, D and Vaughn, BP and Khoruts, A and Knights, D}, title = {Metagenomic source tracking after microbiota transplant therapy.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2487840}, pmid = {40229213}, issn = {1949-0984}, mesh = {Humans ; *Metagenomics/methods ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Colitis, Ulcerative/therapy/microbiology ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Bayes Theorem ; Feces/microbiology ; }, abstract = {Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.}, } @article {pmid40228816, year = {2025}, author = {Chen, J and Liu, X and Bai, Y and Tang, X and Xue, K and Zhu, Z and Liu, W and Wang, J and Wang, C and Qiao, H and Dang, E and Yin, W and Wang, G and Shao, S}, title = {Tonsillar microbiota alterations contribute to immune responses in psoriasis by skewing aged neutrophils.}, journal = {The British journal of dermatology}, volume = {193}, number = {2}, pages = {310-321}, doi = {10.1093/bjd/ljaf134}, pmid = {40228816}, issn = {1365-2133}, support = {82322057//National Natural Science Foundation of China/ ; 82230105//National Natural Science Foundation of China/ ; 82273519//National Natural Science Foundation of China/ ; 2022YFC3601800//National Key R&D Program of China/ ; 2022ZDLSF03-14//Shaanxi Scientific Research/ ; }, mesh = {Humans ; *Psoriasis/immunology/microbiology ; *Neutrophils/immunology ; Male ; Female ; *Palatine Tonsil/microbiology/immunology ; Middle Aged ; Adult ; *Microbiota/immunology ; Case-Control Studies ; Fatty Acids, Volatile/blood/metabolism ; RNA, Ribosomal, 16S ; Cellular Senescence/immunology ; Aged ; }, abstract = {BACKGROUND: The interplay between microbiota and the onset of immune-mediated diseases is increasingly coming to light. However, the role of tonsillar microbiota in cutaneous inflammation remains largely unknown.

OBJECTIVES: To determine how the tonsillar microbiota influences skin inflammation in psoriasis and to uncover the underlying molecular mechanisms.

METHODS: Tonsillar microbiota samples were collected from 24 healthy control individuals and 28 patients with psoriasis. Microbial community composition was analysed with 16S rRNA and metagenomic sequencing. Serum levels of short-chain fatty acids (SCFAs) were measured via liquid chromatography-mass spectrometry in 10 healthy control participants and 14 patients with psoriasis. Peripheral blood neutrophils from both groups were then exposed to a representative microbial metabolite and key proinflammatory markers evaluated using functional immune assays.

RESULTS: We found significant alterations in the diversity and composition of the tonsillar microbial community in patients with psoriasis, with an increased prevalence of Bacteroidales and a decreased prevalence of Burkholderiales, Micrococcales and Pasteurellales relative to healthy control participants. Notably, a marked reduction in Rothia mucilaginosa correlated inversely with systemic inflammation (neutrophil-to-lymphocyte ratio) and disease severity (Psoriasis Area and Severity Index). Metagenomic analysis revealed disruptions in pathways critical to SCFA production, including propanoate, pyruvate and butanoate metabolism, which was supported by the significantly lower serum SCFA levels found in patients with psoriasis. Functional assays demonstrated that SCFAs inhibited neutrophil ageing, proinflammatory cytokine secretion and neutrophil extracellular trap formation.

CONCLUSIONS: Our findings reveal that changes in tonsillar microbiota and their metabolic outputs contribute to psoriasis by modulating -immune responses, with potential clinical implications.}, } @article {pmid40228693, year = {2025}, author = {Ma, JY and Liu, JH and Chen, CZ and Zhang, YZ and Guo, ZS and Song, MP and Jiang, F and Chai, ZT and Li, Z and Lv, SX and Zhen, YJ and Wang, L and Liang, ZL and Jiang, ZY}, title = {Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.}, journal = {Environmental research}, volume = {277}, number = {}, pages = {121559}, doi = {10.1016/j.envres.2025.121559}, pmid = {40228693}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology/chemistry ; Aquaculture ; *Carbon/metabolism ; *Kelp ; Microbiota ; *Carbon Cycle ; }, abstract = {The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.}, } @article {pmid40226542, year = {2025}, author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B}, title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19260}, pmid = {40226542}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Sympatry ; Bacteroidetes/genetics/isolation & purification ; }, abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.}, } @article {pmid40223739, year = {2025}, author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A}, title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {31}, number = {4}, pages = {212-218}, pmid = {40223739}, issn = {1998-4049}, mesh = {Humans ; *Colitis, Ulcerative/virology/microbiology/epidemiology ; Saudi Arabia/epidemiology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Child ; *Virome/genetics ; Feces/virology/microbiology ; Adolescent ; Case-Control Studies ; *Bacteriophages/genetics/isolation & purification ; Metagenomics ; }, abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.

METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.

RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4 , uncultured_crAssphage, Staphylococcus_phage_SPbeta-like , Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.

CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.}, } @article {pmid40223703, year = {2025}, author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H}, title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.}, journal = {Environmental science & technology}, volume = {59}, number = {15}, pages = {7550-7560}, doi = {10.1021/acs.est.5c00306}, pmid = {40223703}, issn = {1520-5851}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; Soil/chemistry ; Soil Pollutants/metabolism ; Bacteria/metabolism ; Microbiota ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.}, } @article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, pmid = {40223273}, issn = {1738-8872}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics/trends ; Multiomics/trends ; *Host Microbial Interactions/physiology ; *Translational Research, Biomedical/methods/trends ; Precision Medicine/methods/trends ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, } @article {pmid40223231, year = {2025}, author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S}, title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2489154}, pmid = {40223231}, issn = {2150-5608}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; }, abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.}, } @article {pmid40222673, year = {2025}, author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL}, title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.}, journal = {Journal of dairy science}, volume = {108}, number = {6}, pages = {5705-5718}, doi = {10.3168/jds.2025-26395}, pmid = {40222673}, issn = {1525-3198}, mesh = {Animals ; *Milk/microbiology ; *Bacteriocins/pharmacology ; Pasteurization ; *Microbiota/drug effects ; Food Preservation/methods ; }, abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2× MIC (low concentration), and treatment group with the addition of 4× MIC RSQ01 (high concentration). Integrated 16S ribosomal DNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, whereas probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and AA) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.}, } @article {pmid40222470, year = {2025}, author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z}, title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.}, journal = {Environmental research}, volume = {277}, number = {}, pages = {121602}, doi = {10.1016/j.envres.2025.121602}, pmid = {40222470}, issn = {1096-0953}, mesh = {*Ammonia/metabolism ; *Geologic Sediments/microbiology ; *Wetlands ; Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics ; Oxidation-Reduction ; Metagenome ; Microbiota ; }, abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2 %) was higher than ammonia-oxidizing bacteria (AOB, 12.0 %), but lower than ammonia-oxidizing archaea (AOA, 64.8 %). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.}, } @article {pmid40221653, year = {2025}, author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ}, title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {26}, pmid = {40221653}, issn = {2730-6844}, mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.

DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.}, } @article {pmid40221512, year = {2025}, author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y}, title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12568}, pmid = {40221512}, issn = {2045-2322}, support = {82104236//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; }, abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.}, } @article {pmid40221450, year = {2025}, author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW}, title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {57}, pmid = {40221450}, issn = {2055-5008}, support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.}, } @article {pmid40220806, year = {2025}, author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q}, title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.}, journal = {International journal of biological macromolecules}, volume = {309}, number = {Pt 3}, pages = {142983}, doi = {10.1016/j.ijbiomac.2025.142983}, pmid = {40220806}, issn = {1879-0003}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Rats ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics/drug effects ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Humans ; *Genes, Bacterial ; Male ; *Drug Resistance, Bacterial/genetics/drug effects ; Bacteria/genetics/drug effects ; }, abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.}, } @article {pmid40220715, year = {2025}, author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X}, title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.}, journal = {EBioMedicine}, volume = {115}, number = {}, pages = {105686}, pmid = {40220715}, issn = {2352-3964}, mesh = {*Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; Animals ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Disease Models, Animal ; *Pulmonary Arterial Hypertension/etiology/microbiology ; Metagenomics/methods ; Female ; Middle Aged ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.

METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.

FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.

INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.

FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).}, } @article {pmid40220550, year = {2025}, author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E}, title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.}, journal = {Archives of oral biology}, volume = {175}, number = {}, pages = {106251}, doi = {10.1016/j.archoralbio.2025.106251}, pmid = {40220550}, issn = {1879-1506}, mesh = {Humans ; *Metabolic Syndrome/microbiology ; Brazil/epidemiology ; Male ; Female ; *Saliva/microbiology ; Middle Aged ; Adult ; *Microbiota ; Body Mass Index ; Waist Circumference ; Triglycerides/blood ; Obesity ; }, abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.}, } @article {pmid40216789, year = {2025}, author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG}, title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3469}, pmid = {40216789}, issn = {2041-1723}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; }, abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.}, } @article {pmid40216686, year = {2025}, author = {Fan, Q and Zhang, Y and Lian, J and Liang, D and Yu, J and Liu, X and Zhang, N}, title = {Screening and community succession and functional prediction of high-efficiency degradation microbial communities for rice straw at low-temperature.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {2}, pages = {20}, pmid = {40216686}, issn = {1433-4909}, support = {2023YFD2100803//National Key R&D Programme Project of China/ ; }, mesh = {*Oryza/microbiology/metabolism ; *Microbiota ; *Cold Temperature ; Lignin/metabolism ; }, abstract = {Traditional straw return relies on microbial degradation, but cold winters delay it, risking crops. Therefore, a microbial community adapted to rice straw degradation in cold regions was constructed by restrictive consecutively sub-cultured under low-temperature limitations. The capabilities of the microbial community, such as adaptability, stability, and degradation power, were evaluated by analyzing straw degradation features, Characterization experiments and lignocellulose enzyme activities across multiple generations. 16S amplicon sequencing was used to monitor the changes in its structure over generations. Metagenomic sequencing uses CAZy and KEGG to classify gene functions. The results showed that the highest degradation efficiencies and enzyme activities were observed in the E and F generations, dominated by Proteobacteria, Bacteroidetes, and Fungi The stable microbial community was designated as LJ-7. Metagenomic analysis showed that functional genes of LJ-7 were mainly concentrated in glycoside hydrolase (GHs) and glycosyl transferase (GTs) related genes which contained many fiber and lignin-degrading enzyme genes. It is speculated that microbial enzymes degrade straw by breaking down its complex structure into monosaccharides or metabolizing quinone compounds for energy. This experiment successfully screened a microbial community capable of degrading rice straw at low temperatures, thus offering novel research insights and pathways for straw degradation in cold conditions.}, } @article {pmid40216167, year = {2025}, author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW}, title = {Investigating the bidirectional interactions between senotherapeutic agents and human gut microbiota.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {209}, number = {}, pages = {107098}, doi = {10.1016/j.ejps.2025.107098}, pmid = {40216167}, issn = {1879-0720}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Quercetin/pharmacology ; *Senotherapeutics/pharmacology ; Dasatinib/pharmacology ; Sirolimus/pharmacology ; Flavonoids/pharmacology ; Bacteria/drug effects/genetics ; Adult ; Male ; Flavonols/pharmacology ; Female ; Middle Aged ; Aging/drug effects ; }, abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.}, } @article {pmid40215877, year = {2025}, author = {Saeed, M and Al-Khalaifah, H and Al-Nasser, A and Al-Surrayai, T}, title = {Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105130}, pmid = {40215877}, issn = {1525-3171}, mesh = {Animals ; *Probiotics/administration & dosage ; *Chickens/physiology/growth & development ; Animal Feed/analysis ; Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena ; *Lactobacillus plantarum/chemistry ; *Animal Husbandry/methods ; }, abstract = {The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.}, } @article {pmid40214404, year = {2025}, author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, MØ and Rudi, K}, title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.}, journal = {Environmental science & technology}, volume = {59}, number = {15}, pages = {7517-7529}, pmid = {40214404}, issn = {1520-5851}, mesh = {Animals ; Aquaculture ; Archaea ; Ecosystem ; Iceland ; *Microbiota ; Norway ; *Aquatic Organisms/microbiology ; }, abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.}, } @article {pmid40212922, year = {2025}, author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H}, title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71221}, pmid = {40212922}, issn = {2045-7758}, abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.}, } @article {pmid40211688, year = {2025}, author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX}, title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.}, journal = {Molecular ecology}, volume = {34}, number = {9}, pages = {e17751}, doi = {10.1111/mec.17751}, pmid = {40211688}, issn = {1365-294X}, support = {2021YFD1400900//National Key R&D Program of China/ ; }, mesh = {Animals ; *Coleoptera/microbiology/genetics/growth & development ; *Microbiota/genetics ; Larva/microbiology ; Bacteria/genetics/classification ; Gastrointestinal Microbiome/genetics ; Wood ; Life Cycle Stages ; Fungi/genetics/classification ; }, abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.}, } @article {pmid40211121, year = {2025}, author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, É and Pombo, GDV and Santana, MHA}, title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {359}, pmid = {40211121}, issn = {1471-2164}, support = {2021/03265-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40210868, year = {2025}, author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA}, title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3434}, pmid = {40210868}, issn = {2041-1723}, support = {R01 DK140854/DK/NIDDK NIH HHS/United States ; 1R01DK140854//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; }, abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.}, } @article {pmid40210629, year = {2025}, author = {Park, JW and Yun, YE and Cho, JA and Yoon, SI and In, SA and Park, EJ and Kim, MS}, title = {Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3427}, pmid = {40210629}, issn = {2041-1723}, support = {2020R1A5A8017671//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009664//National Research Foundation of Korea (NRF)/ ; 2018R1D1A3B07050366//National Research Foundation of Korea (NRF)/ ; 2021R1F1A1064222//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Virome/genetics ; *Vegetables/virology ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Plant Leaves/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; }, abstract = {Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 10[7] viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.}, } @article {pmid40210439, year = {2025}, author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS}, title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.}, journal = {Genome research}, volume = {35}, number = {5}, pages = {1247-1260}, pmid = {40210439}, issn = {1549-5469}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Genetic Variation ; *Bacteria/genetics/classification ; }, abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.}, } @article {pmid40210403, year = {2025}, author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH}, title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.}, journal = {Food microbiology}, volume = {130}, number = {}, pages = {104780}, doi = {10.1016/j.fm.2025.104780}, pmid = {40210403}, issn = {1095-9998}, mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; }, abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.}, } @article {pmid40210162, year = {2025}, author = {Gao, X and Yuan, S and Li, X and Xing, W}, title = {Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126213}, doi = {10.1016/j.envpol.2025.126213}, pmid = {40210162}, issn = {1873-6424}, mesh = {*Geologic Sediments/microbiology ; *Nitrogen Cycle ; *Microplastics/toxicity ; *Water Pollutants, Chemical ; *Carbon Cycle ; Carbon/metabolism ; Nitrogen/metabolism ; Microbiota ; }, abstract = {Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5 % w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.}, } @article {pmid40209677, year = {2025}, author = {Lin, Y and Lau, HC and Liu, C and Ding, X and Sun, Y and Rong, J and Zhang, X and Wang, L and Yuan, K and Miao, Y and Wu, WK and Wong, SH and Sung, JJ and Yu, J}, title = {Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact.}, journal = {Cell host & microbe}, volume = {33}, number = {4}, pages = {589-601.e3}, doi = {10.1016/j.chom.2025.03.012}, pmid = {40209677}, issn = {1934-6069}, mesh = {Humans ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Gastrointestinal Microbiome ; Cohort Studies ; Metagenome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Aged ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor ; ROC Curve ; }, abstract = {Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.}, } @article {pmid40209382, year = {2025}, author = {Su, C and Kang, J and Liu, S and Li, C}, title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144192}, doi = {10.1016/j.foodchem.2025.144192}, pmid = {40209382}, issn = {1873-7072}, mesh = {*Morinda/microbiology/chemistry/growth & development/metabolism ; *Fruit/microbiology/chemistry/growth & development/metabolism ; *Fruit and Vegetable Juices/analysis/microbiology ; *Microbiota ; Fermentation ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Volatile Organic Compounds/metabolism/chemistry ; Taste ; }, abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.}, } @article {pmid40209373, year = {2025}, author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J}, title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144178}, doi = {10.1016/j.foodchem.2025.144178}, pmid = {40209373}, issn = {1873-7072}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Stichopus/metabolism/microbiology/chemistry ; *Sea Cucumbers/metabolism/microbiology ; Polysaccharides/metabolism/analysis ; Collagen/metabolism ; }, abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.}, } @article {pmid40207938, year = {2025}, author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ}, title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.}, journal = {mBio}, volume = {16}, number = {5}, pages = {e0069925}, pmid = {40207938}, issn = {2150-7511}, support = {FRN-142349//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Eukaryota/genetics ; *Computational Biology/methods ; *Blastocystis/genetics ; Gastrointestinal Microbiome/genetics ; Metagenome ; Whole Genome Sequencing ; Software ; }, abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.}, } @article {pmid40207877, year = {2025}, author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W}, title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70336}, doi = {10.1002/jmv.70336}, pmid = {40207877}, issn = {1096-9071}, support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; }, mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; Adult ; Aged ; Longitudinal Studies ; }, abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.}, } @article {pmid40207161, year = {2025}, author = {Helmi, NR}, title = {Exploring the diversity and antimicrobial potential of actinomycetes isolated from different environments in Saudi Arabia: a systematic review.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1568899}, pmid = {40207161}, issn = {1664-302X}, abstract = {The increasing prevalence of antimicrobial resistance (AMR) presents a significant global health challenge, underscoring the urgent need for novel antimicrobial agents. Actinomycetes, particularly Streptomyces species, are well known for synthesizing bioactive compounds with antibacterial, antifungal, and antiviral properties. This review explores the diversity and antimicrobial potential of actinomycetes from Saudi Arabia's unique ecosystems, including terrestrial (soil, rhizosphere), aquatic (marine, freshwater), extreme (deserts, caves, hot springs, mountains, and mangroves), and other unique environments. The adaptation of these microorganisms to harsh environmental conditions has driven the evolution of unique strains with enhanced biosynthetic capacities. Several studies have demonstrated their antimicrobial efficacy against multidrug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Pseudomonas aeruginosa, and Candida albicans. However, challenges in actinomycete research persist, including difficulties in culturing rare strains, limited genomic characterization, and high production costs. Recent advancements, such as genome mining, metagenomics, AI-driven bioinformatics, and CRISPR-based gene activation, offer promising avenues for unlocking novel antimicrobial compounds. Additionally, synthetic biology, advanced fermentation technologies, and nanotechnology-based drug delivery systems are enhancing the industrial scalability of actinomycete-derived antibiotics. Beyond antimicrobials, actinomycete-derived compounds show potential applications in oncology, immunotherapy, and agriculture. Alternative therapeutic strategies, including quorum sensing inhibitors, phage therapy, and combination therapies, are being explored to combat AMR. Cutting-edge analytical techniques, such as mass spectrometry, liquid chromatography, and nuclear magnetic resonance spectroscopy (NMR), are essential for structural elucidation and mechanism characterization of new bioactive compounds. To harness Saudi Arabia's microbial biodiversity effectively, interdisciplinary collaborations between microbiologists, biotechnologists, and pharmaceutical industries are crucial. Sustainable bioprospecting and advanced bioprocessing strategies will facilitate the translation of actinomycete-derived bioactive compounds into clinically viable therapeutics. Expanding research efforts into underexplored Saudi ecosystems can lead to groundbreaking discoveries in antibiotic development and beyond.}, } @article {pmid40205678, year = {2025}, author = {He, Y and Zhao, G and Ouyang, X and Wang, S and Chen, Y and Li, C and He, Y and Gao, J and Han, S and Zhao, J and Wang, J and Wang, C}, title = {Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2489072}, pmid = {40205678}, issn = {1949-0984}, mesh = {Animals ; Mice ; Gastrointestinal Microbiome/drug effects/radiation effects ; *Creatine/metabolism/pharmacology/administration & dosage ; *Ferroptosis/drug effects/radiation effects ; Mice, Inbred C57BL ; Male ; *Intestines/radiation effects/microbiology ; *Radiation-Protective Agents/metabolism/administration & dosage ; Radiation, Ionizing ; Feces/microbiology ; Enterocytes/radiation effects/metabolism ; }, abstract = {Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.}, } @article {pmid40205473, year = {2025}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V}, title = {Running against the clock: exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40205473}, issn = {1574-6941}, support = {//DGAPA/ ; IG200319//UNAM/ ; //Instituto de Ecología, Universidad Nacional Autónoma de México/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; Desert Climate ; *Microbiota/genetics ; Phylogeny ; Ecosystem ; Groundwater/microbiology ; }, abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas (PR) and Archean Domes (AD). Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from PR and AD: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and AD: Halanaerobium sp. (63%) and D. halophilus (60%). Furthermore, metagenome-assembled genomes from Ectothiorhodospira genus were found in both AD and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the AD system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.}, } @article {pmid40204761, year = {2025}, author = {Li, F and Hooi, SL and Choo, YM and Teh, CSJ and Toh, KY and Lim, LWZ and Lee, YQ and Chong, CW and Ahmad Kamar, A}, title = {Progression of gut microbiome in preterm infants during the first three months.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12104}, pmid = {40204761}, issn = {2045-2322}, support = {IF047-2021//International Funding/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; Prospective Studies ; *Bacteria/genetics/classification ; Infant ; Gestational Age ; Bifidobacterium/genetics/isolation & purification ; Meconium/microbiology ; Metagenomics ; }, abstract = {The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.}, } @article {pmid40203979, year = {2025}, author = {Genitsaris, S and Stefanidou, N and Kourkoutmani, P and Michaloudi, E and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M}, title = {Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.}, journal = {Environmental research}, volume = {277}, number = {}, pages = {121563}, doi = {10.1016/j.envres.2025.121563}, pmid = {40203979}, issn = {1096-0953}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; *Plankton/metabolism ; *Bacteria/metabolism/genetics ; RNA, Ribosomal, 16S ; Microbiota ; Seawater/microbiology ; }, abstract = {Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.}, } @article {pmid40202719, year = {2025}, author = {Huang, Z and Liu, C and Zhao, X and Guo, Y}, title = {The effect of elevated levels of the gut metabolite TMAO on glucose metabolism after sleeve gastrectomy.}, journal = {Archives of physiology and biochemistry}, volume = {131}, number = {4}, pages = {691-700}, doi = {10.1080/13813455.2025.2489721}, pmid = {40202719}, issn = {1744-4160}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Gastrectomy ; *Methylamines/metabolism/blood ; Mice ; Male ; Liver/metabolism ; *Glucose/metabolism ; Mice, Inbred C57BL ; *Obesity/metabolism/surgery/microbiology ; Forkhead Box Protein O1/metabolism/genetics ; Glycogen/metabolism ; Oxygenases ; }, abstract = {PURPOSE: Bariatric surgery can effectively alleviate obesity and diabetes by regulation of the gut microbiota. This study aimed to investigate the change in the gut microbiota metabolite TMAO and to explore its effect on glucose metabolism after sleeve gastrectomy (SG).

MATERIALS AND METHODS: Diet-induced obesity mouse models were established, and the mice were randomly divided into four groups: an SG group, a sham-operated group pair-fed with the SG group (PF), a sham-operated group fed ad libitum (AL), and a lean control group (C). At 10 weeks post-surgery, the changes in glycogen content of liver, gut microbiota and the level of FMO3 in the liver were evaluated, and their correlation with TMAO production was analysed. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured.

RESULTS: At 10 weeks post-surgery, hepatocyte glycogen levels were restored, and serum TMA and TMAO levels were significantly increased. Faecal metagenomic sequencing results showed that the abundances of Ruminococcaceae and Lachnospiraceae, which were positively correlated with TMAO production, were significantly increased after surgery. While the changes in FMO3, the key enzyme producing TMAO in the liver was found decreased significantly after SG. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Inconsistent with the changing trend of TMAO, the expression of PERK, FOXO1, PCK, and G6PC significantly decreased after SG.

CONCLUSIONS: SG can significantly reduce obesity and restore glucose metabolism. After surgery, TMAO metabolites increased in a microbiota-dependent manner.}, } @article {pmid40202375, year = {2025}, author = {Pan, C and Xu, P and Yuan, M and Wei, S and Lu, Y and Lu, H and Zhang, W}, title = {Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70344}, doi = {10.1002/jmv.70344}, pmid = {40202375}, issn = {1096-9071}, support = {//This study was supported by the Zhenjiang Science and Technology Innovation Funds-Clinical Medicine Key Laboratory and Scientific Research Project of Health Commission of Jiangsu Province./ ; }, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Virome ; Feces/virology ; *Breast Feeding ; Female ; Male ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; *Feeding Behavior ; Bacteriophages/genetics/classification/isolation & purification ; Milk, Human/virology ; *Gastrointestinal Tract/virology ; }, abstract = {The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.}, } @article {pmid40201423, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J}, title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf049}, pmid = {40201423}, issn = {2730-6151}, abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.}, } @article {pmid40199830, year = {2025}, author = {Singh, P and Haldhar, P and Das, T and Chaubey, G and Gupta, MK and Kumar, B}, title = {Thermal Stress and Its Effects on the Gut Microbiome of Parthenium Beetles.}, journal = {Archives of insect biochemistry and physiology}, volume = {118}, number = {4}, pages = {e70058}, doi = {10.1002/arch.70058}, pmid = {40199830}, issn = {1520-6327}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Stress, Physiological ; Bacteria/classification/isolation & purification/genetics ; Hot Temperature ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The gut microbiota plays a vital role in nutrient and energy utilization, as well as in the host's ability to adapt its immune system to environmental changes. As a biological control agent for the invasive Parthenium weed, the Parthenium beetle Zygogramma bicolorata (Z. bicolorata) Pallister is often exposed to fluctuating temperatures, which may induce stress in its natural habitat. This study utilized 16S amplicon sequencing to explore the impact of temperature stress on the gut microbiome of Z. bicolorata under cold (15°C), control (27°C), and hot (35°C) conditions. A total of 11 bacterial phyla and 149 genera were identified, with Firmicutes, Proteobacteria, and Cyanobacteria being the most abundant. Temperature treatments significantly influenced the diversity of the gut microbiota, as evidenced by alpha diversity measures. Principal coordinate analysis further revealed substantial variations in microbiome composition across the different temperature conditions. Additionally, PICRUSt2 analysis suggested that the gut microbiota is linked to metagenomic functions related to amino acid and carbohydrate transport, inorganic ion metabolism, and cellular processes. Our findings suggest that thermal stress alters the gut microbiome of Parthenium beetles, offering new insights into how these beetles may have ecologically adapted to temperature fluctuations, while also highlighting the potential role of gut microbes in maintaining beetle health under environmental stress.}, } @article {pmid40197788, year = {2025}, author = {Arenas-Montes, J and Alcala-Diaz, JF and Garcia-Fernandez, H and Gutierrez-Mariscal, FM and Lopez-Moreno, A and Luque-Cordoba, D and Arenas-de Larriva, AP and Torres-Peña, JD and Luque, RM and Prodam, F and Priego-Capote, F and Delgado-Lista, J and Lopez-Miranda, J and Camargo, A}, title = {A microbiota pattern associated with cardiovascular events in secondary prevention: the CORDIOPREV study.}, journal = {European heart journal}, volume = {46}, number = {22}, pages = {2104-2115}, doi = {10.1093/eurheartj/ehaf181}, pmid = {40197788}, issn = {1522-9645}, support = {//Fundacion Patrimonio Comunal Olivarero/ ; //CEAS/ ; //Centro de Excelencia en Investigacion sobre Aceite de Oliva/ ; CVI-7450//Junta de Andalucia/ ; //Diputaciones de Jaen y Córdoba/ ; //Ministerio de Medio Ambiente, Medio Rural y Marino/ ; //Spanish Government/ ; AGL2012/39615//Ministerio de Ciencia e Innovación, Spain/ ; //MCIN/AEI/10.13039/501100011033/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI-0055-2021//Consejería de Salud y Familias, Junta de Andalucía/ ; //Consejeria de Innovación, Ciencia y Empresa, Proyectos de Investigación de Excelencia/ ; //European Union/ ; CP14/00114//Programa Miguel-Servet/ ; //Servicio Andaluz de Salud-Junta de Andalucia/ ; C1-0001-2022//Nicolas Monardes Programme Contract/ ; PY20_00256//Junta de Andalucia/ ; PIE14/00005//Ministerio de Ciencia e Innovación, Spain/ ; PIE14/00031//Ministerio de Ciencia e Innovación, Spain/ ; AGL2015-67896-P//Ministerio de Ciencia e Innovación, Spain/ ; PID2019-104362RB//Ministerio de Ciencia e Innovación, Spain/ ; PID2019-104362RB-I00//Ministerio de Ciencia e Innovación, Spain/ ; PI19/00299//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; CPII19/00007//Programa Miguel-Servet/ ; }, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Secondary Prevention/methods ; Aged ; *Cardiovascular Diseases/prevention & control/microbiology ; Feces/microbiology ; *Coronary Disease/microbiology/prevention & control ; }, abstract = {BACKGROUND AND AIMS: Preventing new cardiovascular events in patients with established cardiovascular disease (CVD) is a daunting task for clinicians. Intestinal microbiota may help identify patients at risk, thus improving the strategies of secondary prevention. The aim of this study was to evaluate the baseline differences between the gut microbiota from coronary heart disease (CHD) patients suffering new major adverse cardiovascular events (MACEs) in the following 7 years, compared with CHD patients who did not undergo new MACE in this period, and to build a score associated with the risk of suffering new MACE.

METHODS: Within the framework of the CORDIOPREV study, a clinical trial that involved 1002 patients with CHD, intestinal microbiota was examined in patients with available faecal samples (n = 679, 132 MACE), through 16S metagenomics on the Illumina MiSeq and Quiime2 software. Lipopolysaccharide (LPS) was measured using limulus amoebocyte lysate test.

RESULTS: Random survival forest identified 10 bacterial taxa with a higher predictive power for MACE incidence. Receiver operating characteristic curves yielded an area under the curve of 65.2% (59.1%-71.3%) in the training set and 68.6% (59.3%-77.9%) in the validation set. The intestinal microbiota risk score was associated with a MACE incidence hazard ratio of 2.01 (95% confidence interval 1.37-3.22). Lipopolysaccharide analysis showed a greater LPS post-prandial fold change in the MACE group (P = .005).

CONCLUSIONS: These results reinforce the relationship between intestinal microbiota and CVD and suggest that a microbiota profile is associated with MACE in CHD patients, in addition to higher endotoxaemia.}, } @article {pmid40197113, year = {2025}, author = {Karabekmez, ME}, title = {Harnessing Human Holobiome and Meta-Multi-Omics Analyses for Medical Applications.}, journal = {Omics : a journal of integrative biology}, volume = {29}, number = {5}, pages = {179-182}, doi = {10.1089/omi.2025.0024}, pmid = {40197113}, issn = {1557-8100}, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota ; Multiomics ; Precision Medicine ; Proteomics/methods ; }, abstract = {Next-generation sequencing technology has revolutionized all fields of living systems, and its applications almost reinvented some research areas including metagenomics. The microbiotas in our body, including those of the oral, nasal, ocular, alveolar, skin regions, and particularly gut microbiota, have close linkages with our health status. Maturation of experimental techniques for metagenomics has been followed by other related omics platforms, for example, metatranscriptomics, metaproteomics, and all possible metacounterparts of multiomics studies. Now, we are on the eve of a meta-multi-omics era for the analysis of human holobiome in medical research. This era will help buttress the current efforts for systems medicine by illuminating the relationships between human holobiome and health or all human diseases including not only cancers but also infectious diseases, autoimmune diseases, obesity, aging, genetic disorders, and psychiatric conditions. Equally important, meta-multi-omics era is also poised to inform the determinants of human health and, by extension, help build individually tailored precision medicine interventions.}, } @article {pmid40197053, year = {2025}, author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A}, title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0116624}, pmid = {40197053}, issn = {2379-5077}, support = {N11A650143//National Research Council of Thailand/ ; RA-MF 47/64//Faculty of Medicine, Chulalongkorn University/ ; HEA663000027//Chulalongkorn University/ ; }, mesh = {*DNA, Fungal/isolation & purification/genetics ; Humans ; *Metagenomics/methods ; *Fungi/genetics ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopores ; }, abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.

IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.}, } @article {pmid40197051, year = {2025}, author = {Shamash, M and Sinha, A and Maurice, CF}, title = {Improving gut virome comparisons using predicted phage host information.}, journal = {mSystems}, volume = {10}, number = {5}, pages = {e0136424}, pmid = {40197051}, issn = {2379-5077}, mesh = {*Bacteriophages/genetics/classification/physiology ; *Virome/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Feces/virology/microbiology ; Metagenomics/methods ; Computational Biology/methods ; Bacteria/virology ; }, abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.

IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.}, } @article {pmid40196042, year = {2025}, author = {Wang, H and Zhu, W and Lei, J and Liu, Z and Cai, Y and Wang, S and Li, A}, title = {Gut microbiome differences and disease risk in colorectal cancer relatives and healthy individuals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1573216}, pmid = {40196042}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Risk Factors ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; Cohort Studies ; Family ; Whole Genome Sequencing ; }, abstract = {Given the heightened focus on high-risk populations, this study aimed to provide insights into early susceptibility and preventive strategies for colorectal cancer (CRC) by focusing on high-risk populations. In this research, fecal samples from 1,647 individuals across three discovery cohorts and nine external validation cohorts were sequenced using whole-genome metagenomic sequencing. A prediction model based on random forest was constructed using the nine external cohorts and independently validated with the three discovery cohorts. A disease probability (POD) model based on microbial biomarkers was developed to assess CRC risk. We found that the gut microbiome composition of CRC relatives differed from that of controls, with enrichment of species such as Fusobacterium and Bacteroides and a reduction in beneficial genera like Coprococcus and Roseburia. Additionally, dietary red meat intake emerged as a risk factor. The POD model indicated an elevated risk of CRC in unaffected relatives. The findings suggest that the POD for CRC may be increased in unaffected relatives or individuals living in shared environments, although this difference did not reach statistical significance. Our study introduces a novel framework for assessing the risk of colorectal cancer in ostensibly healthy individuals.}, } @article {pmid40195460, year = {2025}, author = {Bhagat, NR and Bharti, VK and Shukla, G and Rishi, P and Chaurasia, OP}, title = {Gut bacteriome dynamics in high altitude-adapted chicken lines: a key to future poultry therapeutics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11910}, pmid = {40195460}, issn = {2045-2322}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Altitude ; Metagenomics/methods ; *Bacteria/genetics/classification ; *Adaptation, Physiological ; Metagenome ; }, abstract = {High-altitude-adapted chickens harbor a unique gut bacteriome essential for their survival under extremely cold and hypoxic environment, however, little is known about their population and functional dynamics, limiting their application in poultry production. Hence, this study employed amplicon-based metagenomics to examine the gut bacterial diversity and their functional profile in two high-altitude-adapted chicken lines, e.g. LEHBRO-1 and LEHBRO-3. The results revealed significant variations in taxonomic abundance at the phylum level, with Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria predominating in LEHBRO-1, whereas Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria predominated in LEHBRO-3. Genus-level diversity and Linear Discriminant Analysis Effect Size (LEfSe) biomarker analysis also substantiated the differences in the gut bacterial communities between the two chicken lines. Furthermore, functional profiling revealed enrichment of carbohydrate, nucleotide, lipid, amino acid, fatty acid, energy, and glycan metabolic pathways in the gut bacteriomes of these high-altitude chicken lines. The Statistical Analysis of Metagenomic Profiles (STAMP) for metabolic profiling identified a significant difference in purine and protein metabolism between these two chicken lines. These findings indicate the unique gut bacteriome and their functional diversity in high-altitude-adapted chickens, which would provide a foundation for future research on gut therapeutics to improve chicken health and productivity in high-altitude areas.}, } @article {pmid40195156, year = {2025}, author = {Sefrji, FO and Abulfaraj, AA and Alshehrei, FM and Al-Andal, A and Alnahari, AA and Tashkandi, M and Baz, L and Barqawi, AA and Almutrafy, AM and Alshareef, SA and Alkhatib, SN and Abuauf, HW and Jalal, RS and Aloufi, AS}, title = {Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.}, journal = {Functional & integrative genomics}, volume = {25}, number = {1}, pages = {82}, pmid = {40195156}, issn = {1438-7948}, mesh = {*Moringa oleifera/microbiology/genetics/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Energy Metabolism/genetics ; Soil Microbiology ; Bacteria/genetics/classification ; Adenosine Triphosphate/metabolism ; Metagenome ; }, abstract = {Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant-microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.}, } @article {pmid40194944, year = {2025}, author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F}, title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40194944}, issn = {1574-6941}, support = {//University of Adelaide/ ; }, mesh = {Animals ; Female ; *Lactation ; *Tachyglossidae/microbiology/physiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Animals, Zoo/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Reproduction ; }, abstract = {Monotreme and marsupial development is characterized by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programmes in the future.}, } @article {pmid40193404, year = {2025}, author = {Aroney, STN and Newell, RJP and Nissen, JN and Camargo, AP and Tyson, GW and Woodcroft, BJ}, title = {CoverM: read alignment statistics for metagenomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {4}, pages = {}, pmid = {40193404}, issn = {1367-4811}, support = {2022070//EMERGE National Science Foundation/ ; DE-SC0004632//Genomic Science Program of the United States Department of Energy/ ; }, mesh = {*Metabolomics/methods ; *Biostatistics/methods ; *Microbiota ; *Software Design ; Genome ; }, abstract = {SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.

CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.}, } @article {pmid40193328, year = {2025}, author = {Jagadesan, S and Guda, C}, title = {MetaDAVis: An R shiny application for metagenomic data analysis and visualization.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0319949}, pmid = {40193328}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; *Software ; *Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.}, } @article {pmid40192235, year = {2025}, author = {Jiao, Y and Ren, J and Xie, S and Yuan, N and Shen, J and Yin, H and Wang, J and Guo, H and Cao, J and Wang, X and Wu, D and Zhou, Z and Qi, X}, title = {Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2488105}, pmid = {40192235}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; *Bile Acids and Salts/metabolism ; Mice ; *NF-kappa B/metabolism/genetics ; Signal Transduction/radiation effects ; *Raffinose/metabolism ; Mice, Inbred C57BL ; Whole-Body Irradiation/adverse effects ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fecal Microbiota Transplantation ; Male ; *Acute Radiation Syndrome/microbiology/metabolism ; *Hematopoiesis/radiation effects ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Dysbiosis/microbiology ; }, abstract = {Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.}, } @article {pmid40190795, year = {2025}, author = {Zhang, Y and Dai, Y and Li, J and Cong, W and Zhang, Y and Nie, X and Wu, Q and Xue, Y}, title = {Climate Change and Human Pressure: Assessing the Vulnerability of Snow Leopard (Panthera uncia) Habitat Integrated With Prey Distribution on the Qinghai-Tibet Plateau.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71232}, pmid = {40190795}, issn = {2045-7758}, abstract = {Climate change is significantly altering the distribution of large carnivores and their primary prey species, with particular emphasis on the changing prey distribution in high-altitude regions. The Qinghai-Tibet Plateau, known for its rich biodiversity, is highly sensitive to climate change, affecting the habitats of snow leopards (Panthera uncia) and blue sheep (Pseudois nayaur). Our study identified blue sheep as the primary prey of snow leopards through metagenomic analysis and used bioclimatic data and Land Use/Cover Change (LUCC) information to model habitat suitability under three climate scenarios (RCP 2.6, RCP 4.5, and RCP 8.5). Projections showed that under RCP 4.5 and RCP 8.5, snow leopard habitats will decrease by 13.0% and 23.4%, while blue sheep habitats will decrease by 38.3% and 49.7%, respectively. These habitats are expected to shift to higher altitudes, with snow leopards experiencing a more significant shift. Based on these findings, we recommend adjusting protected area boundaries for S1 (Ideal distribution range), establishing ecological corridors for S2 (stepping stone), and implementing targeted measures to mitigate human-wildlife conflicts in S3 (potential conflict area). To protect these species, international efforts to reduce carbon emissions, cross-administrative cooperation, and community-based conservation strategies are essential.}, } @article {pmid40190120, year = {2025}, author = {Aboulalazm, FA and Kazen, AB and deLeon, O and Müller, S and Saravia, FL and Lozada-Fernandez, V and Hadiono, MA and Keyes, RF and Smith, BC and Kellogg, SL and Grobe, JL and Kindel, TL and Kirby, JR}, title = {Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2477819}, pmid = {40190120}, issn = {1949-0984}, support = {F31 DK137415/DK/NIDDK NIH HHS/United States ; R01 HL134850/HL/NHLBI NIH HHS/United States ; R21 AG075501/AG/NIA NIH HHS/United States ; P01 HL084207/HL/NHLBI NIH HHS/United States ; R01 HL158900/HL/NHLBI NIH HHS/United States ; T32 GM080202/GM/NIGMS NIH HHS/United States ; R01 DK133121/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Risperidone/adverse effects ; *Limosilactobacillus reuteri/metabolism ; *Weight Gain/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Antipsychotic Agents/adverse effects ; Probiotics/administration & dosage ; Feces/microbiology ; Energy Metabolism/drug effects ; Bacteria/classification/genetics/isolation & purification/metabolism ; }, abstract = {The role of xenobiotic disruption of microbiota, corresponding dysbiosis, and potential links to host metabolic diseases are of critical importance. In this study, we used a widely prescribed antipsychotic drug, risperidone, known to influence weight gain in humans, to induce weight gain in C57BL/6J female mice. We hypothesized that microbes essential for maintaining gut homeostasis and energy balance would be depleted following treatment with risperidone, leading to enhanced weight gain relative to controls. Thus, we performed metagenomic analyses on stool samples to identify microbes that were excluded in risperidone-treated animals but remained present in controls. We identified multiple taxa including Limosilactobacillus reuteri as a candidate for further study. Oral supplementation with L. reuteri protected against risperidone-induced weight gain (RIWG) and was dependent on cellular production of a specialized metabolite, reutericyclin. Further, synthetic reutericyclin was sufficient to mitigate RIWG. Both synthetic reutericyclin and L. reuteri restored energy balance in the presence of risperidone to mitigate excess weight gain and induce shifts in the microbiome associated with leanness. In total, our results identify reutericyclin production by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.}, } @article {pmid40189749, year = {2025}, author = {Birebent, R and Drubay, D and Alves Costa Silva, C and Marmorino, F and Vitali, G and Piccinno, G and Hurtado, Y and Bonato, A and Belluomini, L and Messaoudene, M and Routy, B and Fidelle, M and Zalcman, G and Mazieres, J and Audigier-Valette, C and Moro-Sibilot, D and Goldwasser, F and Scherpereel, A and Pegliasco, H and Ghiringhelli, F and Reni, A and Barlesi, F and Albiges, L and Planchard, D and Martinez, S and Besse, B and Segata, N and Cremolini, C and Zitvogel, L and Iebba, V and Derosa, L}, title = {Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.}, journal = {Oncoimmunology}, volume = {14}, number = {1}, pages = {2484880}, pmid = {40189749}, issn = {2162-402X}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Dysbiosis/microbiology ; Middle Aged ; *Colorectal Neoplasms/mortality/microbiology/pathology ; Aged ; Prognosis ; *Carcinoma, Non-Small-Cell Lung/mortality/microbiology/pathology ; *Lung Neoplasms/mortality/microbiology/pathology ; Akkermansia/isolation & purification ; *Urogenital Neoplasms/mortality/microbiology/pathology ; }, abstract = {Deviations in the diversity and composition of the gut microbiota are called "gut dysbiosis". They have been linked to various chronic diseases including cancers and resistance to immunotherapy. Stool shotgun based-metagenomics informs on the ecological composition of the gut microbiota and the prevalence of homeostatic bacteria such as Akkermansia muciniphila (Akk), while determination of the serum addressin MAdCAM-1 instructs on endothelial gut barrier dysfunction. Here we examined patient survival during chemo-immuno-therapy in 955 cancer patients across four independent cohorts of non-small cell lung (NSCLC), genitourinary (GU) and colorectal (CRC) cancers, according to hallmarks of gut dysbiosis. We show that Akk prevalence represents a stable and favorable phenotype in NSCLC and CRC cancer patients. Over-dominance of Akk above the healthy threshold was observed in dismal prognosis in NSCLC and GU and mirrored an immunosuppressive gut ecosystem and excessive intestinal epithelial exfoliation in NSCLC. In CRC, the combination of a lack of Akk and low sMAdCAM-1 levels identified a subset comprising 28% of patients with reduced survival, independent of the immunoscore. We conclude that gut dysbiosis hallmarks deserve integration within the diagnosis toolbox in oncological practice.}, } @article {pmid40189708, year = {2025}, author = {Gen-Jiménez, A and Flores-Félix, JD and Rincón-Molina, CI and Manzano-Gómez, LA and Villalobos-Maldonado, JJ and Ruiz-Lau, N and Roca-Couso, R and Ruíz-Valdiviezo, VM and Rincón-Rosales, R}, title = {Native Rhizobium biofertilization enhances yield and quality in Solanum lycopersicum under field conditions.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {4}, pages = {126}, pmid = {40189708}, issn = {1573-0972}, support = {19337.24-P//Tecnológico Nacional de México/ ; }, mesh = {*Solanum lycopersicum/growth & development/microbiology ; *Rhizobium/physiology ; Soil Microbiology ; *Fertilizers ; Soil/chemistry ; Fruit/growth & development ; Nitrogen/analysis/metabolism ; Microbiota ; Agriculture/methods ; }, abstract = {In response to growing concerns about the environmental and economic impacts of chemical fertilizers, this study explores the potential of biofertilization using native Rhizobium strains to enhance the growth, yield, and quality of Solanum lycopersicum (tomato) under field conditions. The experiment assessed the effects of Rhizobium biofertilization on plant performance and soil microbial communities by applying R. calliandrae, R. jaguaris, R. mayense, and a bacterial consortium, in comparison to conventional chemical fertilization. Key parameters such as plant height, fruit yield, macronutrient and micronutrient content, and fruit quality (lycopene and β-carotene levels) were measured. Results showed that R. calliandrae and R. jaguaris significantly enhanced fruit yield, nitrogen, potassium, manganese, and boron levels, while also improving fruit quality compared to the control. The impact of strain inoculation on the structure of the microbial community was also examined. Metataxonomic analysis of rhizospheric soils revealed no significant changes in microbial diversity, indicating that biofertilization with Rhizobium strains promotes plant growth without disrupting the composition of the soil microbiome. These findings suggest that Rhizobium biofertilization is a viable and sustainable alternative to chemical fertilizers, providing benefits to both crop productivity and soil health while minimizing the environmental footprint associated with conventional agricultural practices. The study underscores the importance of carefully selecting bacterial species with complementary functions to maximize the effectiveness of biofertilization strategies.}, } @article {pmid40189564, year = {2025}, author = {He, Y and Zhuo, S and Li, M and Pan, J and Jiang, Y and Hu, Y and Sanford, RA and Lin, Q and Sun, W and Wei, N and Peng, S and Jiang, Z and Li, S and Li, Y and Dong, Y and Shi, L}, title = {Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {94}, pmid = {40189564}, issn = {2049-2618}, support = {42472366, 92051111 and 42272353//National Natural Science Foundation of China/ ; 122-G1323522144//Fundamental Research Funds for the Chinese Central Government via China University of Geosciences (Wuhan)/ ; }, mesh = {*Symbiosis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Folic Acid/biosynthesis ; Ecosystem ; Phylogeny ; Genome, Bacterial ; *Microbiota ; }, abstract = {BACKGROUND: Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B9) were analyzed and assessed.

RESULTS: In the highly alkaline serpentinite-like ecosystem (pH = 10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 ΔfolA. Further assessment of the available CPR genomes (n = 4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.

CONCLUSIONS: This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.}, } @article {pmid40189545, year = {2025}, author = {Serrana, JM and Nascimento, FJA and Dessirier, B and Broman, E and Posselt, M}, title = {Environmental drivers of the resistome across the Baltic Sea.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {92}, pmid = {40189545}, issn = {2049-2618}, mesh = {*Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; *Geologic Sediments/microbiology ; Metagenome ; Salinity ; Anti-Bacterial Agents/pharmacology ; Temperature ; }, abstract = {BACKGROUND: Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

RESULTS: We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.

CONCLUSIONS: We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.}, } @article {pmid40189243, year = {2025}, author = {Chitcharoen, S and Sawaswong, V and Klomkliew, P and Chanchaem, P and Payungporn, S}, title = {Comparative analysis of human gut bacterial microbiota between shallow shotgun metagenomic sequencing and full-length 16S rDNA amplicon sequencing.}, journal = {Bioscience trends}, volume = {19}, number = {2}, pages = {232-242}, doi = {10.5582/bst.2024.01393}, pmid = {40189243}, issn = {1881-7823}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/classification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {The human gut microbiome is increasingly recognized as important to health and disease, influencing immune function, metabolism, mental health, and chronic illnesses. Two widely used, cost-effective, and fast approaches for analyzing gut microbial communities are shallow shotgun metagenomic sequencing (SSMS) and full-length 16S rDNA sequencing. This study compares these methods across 43 stool samples, revealing notable differences in taxonomic and species-level detection. At the genus level, Bacteroides was most abundant in both methods, with Faecalibacterium showing similar trends but Prevotella was more abundant in full-length 16S rDNA. Genera such as Alistipes and Akkermansia were more frequently detected by full-length 16S rDNA, whereas Eubacterium and Roseburia were more prevalent in SSMS. At the species level, Faecalibacterium prausnitzii, a key indicator of gut health, was abundant across both datasets, while Bacteroides vulgatus was more frequently detected by SSMS. Species within Parabacteroides and Bacteroides were primarily detected by 16S rDNA, contrasting with higher SSMS detection of Prevotella copri and Oscillibacter valericigenes. LEfSe analysis identified 18 species (9 species in each method) with significantly different detection between methods, underscoring the impact of methodological choice on microbial diversity and abundance. Differences in classification databases, such as Ribosomal Database Project (RDP) for 16S rDNA and Kraken2 for SSMS, further highlight the influence of database selection on outcomes. These findings emphasize the importance of carefully selecting sequencing methods and bioinformatics tools in microbiome research, as each approach demonstrates unique strengths and limitations in capturing microbial diversity and relative abundances.}, } @article {pmid40188743, year = {2025}, author = {Deng, K and Wang, L and Nguyen, SM and Shrubsole, MJ and Cai, Q and Lipworth, L and Gupta, DK and Zheng, W and Shu, XO and Yu, D}, title = {A dietary pattern promoting gut sulfur metabolism is associated with increased mortality and altered circulating metabolites in low-income American adults.}, journal = {EBioMedicine}, volume = {115}, number = {}, pages = {105690}, pmid = {40188743}, issn = {2352-3964}, support = {R01 HL149779/HL/NHLBI NIH HHS/United States ; U01 CA202979/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Biomarkers ; Black or African American ; *Diet ; *Gastrointestinal Microbiome ; *Metabolome ; Metabolomics/methods ; *Poverty ; Prospective Studies ; *Sulfur/metabolism ; United States/epidemiology ; }, abstract = {BACKGROUND: Excessive hydrogen sulfide in the gut, generated by sulfur-metabolising bacteria from foods, has been linked to intestinal inflammation and human diseases. We aim to investigate the interplay between diet and sulphur-metabolising bacteria in relation to mortality and circulating metabolites in understudied populations.

METHODS: In the Southern Community Cohort Study (SCCS), a prospective cohort of primarily low-income American adults, habitual diets were assessed using a food frequency questionnaire at baseline (2002-2009). A sulfur microbial diet score (SMDS) was developed among 514 Black/African American participants by linking habitual dietary intakes with the abundance of sulfur-metabolising bacteria profiled by faecal shotgun metagenomics. The SMDS was then constructed among all eligible SCCS participants (50,114 Black/African American and 23,923 non-Hispanic White adults), and its associations with mortality outcomes were examined by Cox proportional hazards model and Fine-Grey subdistribution hazard model. The association between SMDS and 1110 circulating metabolites was examined by linear regression among 1688 SCCS participants with untargeted metabolomic profiling of baseline plasma samples.

FINDINGS: Over an average 13.9-year follow-up, SMDS was associated with increased all-cause mortality (HR [95% CI] for the highest vs. lowest quartiles: 1.21 [1.15-1.27]) and cardiovascular disease (1.18 [1.08-1.29]), cancer (1.13 [1.02-1.25]), and gastrointestinal cancer-specific (1.22 [1.00-1.49]) mortality among Black/African American participants (all P-trend<0.05). The associations were largely consistent across participant subgroups. Similar results were observed among non-Hispanic White participants. The SMDS was associated with 112 circulating metabolites, which mediated 36.15% of the SMDS-mortality association (P = 0.002).

INTERPRETATION: A dietary pattern promoting sulfur-metabolising gut bacteria may contribute to increased total and disease mortality in low-income American adults.

FUNDING: This study was funded by the National Institutes of Health, United States, to Vanderbilt University Medical Center, United States, and Anne Potter Wilson Chair endowment to Vanderbilt University, United States.}, } @article {pmid40188549, year = {2025}, author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F}, title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138164}, doi = {10.1016/j.jhazmat.2025.138164}, pmid = {40188549}, issn = {1873-3336}, mesh = {*Zinc Oxide/toxicity ; *Microplastics/toxicity ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil Pollutants/toxicity ; Metagenomics ; *Nanoparticles/toxicity ; Bacteria/drug effects/genetics ; Agriculture ; Fungi/drug effects/genetics ; Soil/chemistry ; *Metal Nanoparticles/toxicity ; }, abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.}, } @article {pmid40187695, year = {2025}, author = {Palumbo, S and Lucarelli, G and Lasorsa, F and Damiano, R and Autorino, R and Aveta, A and Spena, G and Perdonà, S and Russo, P and Giulioni, C and Cafarelli, A and Finati, M and Siracusano, S and Pandolfo, SD}, title = {Urobiome and Inflammation: A Systematic Review on Microbial Imbalances and Diagnostic Tools for Urinary Disorders.}, journal = {Urology}, volume = {200}, number = {}, pages = {206-215}, doi = {10.1016/j.urology.2025.03.050}, pmid = {40187695}, issn = {1527-9995}, mesh = {Humans ; *Cystitis, Interstitial/microbiology/diagnosis ; *Dysbiosis/microbiology/diagnosis ; *Microbiota ; *Urethritis/microbiology/diagnosis ; *Urinary Tract Infections/microbiology/diagnosis ; }, abstract = {OBJECTIVE: To synthesize current knowledge on urobiome alterations, innovative diagnostic advancements, and emerging therapeutic strategies targeting urobiome dysbiosis in inflammatory urinary tract disorders, including urinary tract infections, nongonococcal urethritis, and interstitial cystitis.

METHODS: A systematic review was conducted by screening the most important scientific databases. The search included the keywords: (microbiome) OR (microbial) OR (bacteria) OR (bacterial profile) AND (urine) OR (urinary) AND (first-morning sample) OR (first void). Only original studies in English involving human specimens were considered.

RESULTS: Of the 760 articles initially identified, a final sample of 20 original studies met the inclusion criteria. Disruptions in the urobiome composition were associated with increased colonization by pathogens such as Escherichia coli and Mycoplasma genitalium, resulting in inflammation and recurrent urinary conditions. Advanced diagnostic techniques, including metaproteomics, metagenomics, and point-of-care assays such as Neisseria gonorrhoeae lateral flow assay, demonstrated enhanced capabilities for rapid pathogen detection and differentiation of inflammatory conditions. Therapeutic interventions targeting urobiome dysbiosis, particularly probiotics (Lactobacillus rhamnosus, L. reuteri, L. crispatus), showed promising efficacy in reducing recurrence and inflammation in clinical trials.

CONCLUSION: Urobiome dysbiosis plays a critical role in inflammatory urinary tract disorders. Innovative diagnostic methods and targeted therapeutic approaches, especially probiotics, offer substantial potential to improve patient outcomes. Further research is warranted to refine these strategies and validate their clinical applicability.}, } @article {pmid40187295, year = {2025}, author = {Coskuner-Weber, O and Alpsoy, S and Yolcu, O and Teber, E and de Marco, A and Shumka, S}, title = {Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.}, journal = {Computational biology and chemistry}, volume = {118}, number = {}, pages = {108444}, doi = {10.1016/j.compbiolchem.2025.108444}, pmid = {40187295}, issn = {1476-928X}, mesh = {*Machine Learning ; *Metagenomics ; *Aquaculture ; *Computational Biology ; *Big Data ; Animals ; Fishes ; }, abstract = {The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.}, } @article {pmid40187012, year = {2025}, author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A}, title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105089}, pmid = {40187012}, issn = {1525-3171}, mesh = {Animals ; Pakistan ; *Chickens/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Feces/microbiology ; Metagenomics ; *Bacteria/isolation & purification/classification/genetics ; *Gastrointestinal Microbiome ; Animal Husbandry ; RNA, Bacterial/analysis ; Farms ; }, abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.}, } @article {pmid40185904, year = {2025}, author = {Wang, D and Gui, S and Pu, J and Zhong, X and Yan, L and Li, Z and Tao, X and Yang, D and Zhou, H and Qiao, R and Zhang, H and Cheng, X and Ren, Y and Chen, W and Chen, X and Tao, W and Chen, Y and Chen, X and Liu, Y and Xie, P}, title = {PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders.}, journal = {Molecular psychiatry}, volume = {30}, number = {9}, pages = {4222-4233}, pmid = {40185904}, issn = {1476-5578}, support = {CSTB2024NSCQ-MSX1027//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; CSTB2024NSCQ-QCXMX0033//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; 82371526//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gastrointestinal Microbiome/physiology/genetics ; *Mental Disorders/microbiology ; Animals ; Humans ; Mice ; *Databases, Factual ; Dysbiosis/microbiology ; Rats ; Metagenomics/methods ; }, abstract = {Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info .}, } @article {pmid40185819, year = {2025}, author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S}, title = {Oral microbiome dysbiosis in cryptogenic ischemic stroke patients with high-risk patent foramen ovale.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11535}, pmid = {40185819}, issn = {2045-2322}, support = {286246//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 355532//Research Council of Finland/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; }, mesh = {Humans ; *Foramen Ovale, Patent/complications/microbiology ; Female ; Male ; *Ischemic Stroke/microbiology/etiology/complications ; *Dysbiosis/microbiology/complications ; *Microbiota ; Adult ; Middle Aged ; Saliva/microbiology ; Case-Control Studies ; *Mouth/microbiology ; Risk Factors ; }, abstract = {Patent foramen ovale (PFO) is the most common congenital heart abnormality of foetal origin and has been associated with cryptogenic ischemic stroke (CIS) through several mechanisms, with most theories supporting paradoxical embolism. Other possible but unknown contributing factors, such as the role of the microbiome in PFO-associated strokes, remain unclear. We analysed saliva metagenomes to study the differences in the oral microbiome between young-onset CIS patients with clinically relevant high-risk PFO (n = 52) and those without PFO (n = 52). Age- and sex-matched stroke-free controls (n = 16) with high-risk PFO were included for the comparison. Beta diversity was significantly different between patients and controls with high-risk PFO, but not between patients with and without high-risk PFO. The phylum Ascomycota and class Saccharomycetes were significantly more abundant in patients with high-risk PFO than in those without high-risk PFO. Additionally, the abundance of Lactococcus, including Lactococcus raffinolactis and L. cremoris, was higher in controls with high-risk PFO than in patients with high-risk PFO. These findings highlight that oral dysbiosis and high-risk PFO may form a critical but under-recognized combination in the aetiology of CIS. Future research should focus on elucidating the precise mechanisms of these interactions and developing targeted interventions.}, } @article {pmid40185271, year = {2025}, author = {Guajardo-Leiva, S and Díez, B and Rojas-Fuentes, C and Chnaiderman, J and Castro-Nallar, E and Catril, V and Ampuero, M and Gaggero, A}, title = {From sewage to genomes: Expanding our understanding of the urban and semi-urban wastewater RNA virome.}, journal = {Environmental research}, volume = {276}, number = {}, pages = {121509}, doi = {10.1016/j.envres.2025.121509}, pmid = {40185271}, issn = {1096-0953}, mesh = {*Wastewater/virology ; *Virome ; *Sewage/virology ; *RNA Viruses/genetics ; Chile ; *Genome, Viral ; Phylogeny ; Environmental Monitoring ; RNA, Viral ; Metagenomics ; }, abstract = {Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. In this study, we explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. We identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences from the Orthornavirae kingdom, clustering into 4989 viral species. Using extensive databases of 14,150 family-level representative sequences, we classified 90 % of our sequences at the family level. Our analysis revealed that treatment reduced viral richness and evenness (Shannon index), but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Species turnover, influenced by catchment area and treatment, accounted for 54 % of sample dissimilarities (Weighted Unifrac). Biomarker analysis indicated that families like Astroviridae and Fiersviridae were more abundant in influents, while Reoviridae and Virgaviridae dominated effluents. This suggests that viral resistance to treatment varies and cannot be solely attributed to genome type, size, or morphology. We traced viral genomes through time and space, identifying sequences like the Pepper Mild Mottle Virus (PMMoV) from the Virgaviridae family over large distances and periods, highlighting its wastewater marker potential. High concentrations of human pathogens, such as Rotavirus (Reoviridae) and Human Astrovirus (Astroviridae), were found in both influents and effluents, stressing the need for continuous monitoring, especially for treated wastewater reuse.}, } @article {pmid40185186, year = {2025}, author = {Liu, Y and Pei, Y and Wang, H and Yang, Z}, title = {Lead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {373}, number = {}, pages = {126187}, doi = {10.1016/j.envpol.2025.126187}, pmid = {40185186}, issn = {1873-6424}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Larva/drug effects/metabolism ; *Amidohydrolases/metabolism ; *Lead/toxicity ; *Ranidae ; Bacteria ; }, abstract = {Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.}, } @article {pmid40184632, year = {2025}, author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T}, title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40184632}, issn = {1751-7370}, support = {17212124//Hong Kong GRF/ ; }, mesh = {*Eukaryota/classification/genetics/isolation & purification ; *Sewage/microbiology/virology/parasitology ; *Wastewater/microbiology ; Hong Kong ; Metagenomics ; Animals ; Biodiversity ; Phylogeny ; }, abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analysed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416 044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.}, } @article {pmid40181255, year = {2025}, author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C}, title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {193}, pmid = {40181255}, issn = {1471-2180}, support = {P 32697//Austrian Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS: Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.}, } @article {pmid40180917, year = {2025}, author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA}, title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3204}, pmid = {40180917}, issn = {2041-1723}, support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; }, abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.}, } @article {pmid40180909, year = {2025}, author = {Bedarf, JR and Romano, S and Heinzmann, SS and Duncan, A and Traka, MH and Ng, D and Segovia-Lizano, D and Simon, MC and Narbad, A and Wüllner, U and Hildebrand, F}, title = {A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.}, journal = {NPJ Parkinson's disease}, volume = {11}, number = {1}, pages = {66}, pmid = {40180909}, issn = {2373-8057}, support = {BB/CCG2260/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {Current treatment of Parkinson's Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required. A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD. A prospective, controlled pilot study (DRKS00034528) was conducted on 11 couples (PD patient plus healthy spouse as control (CO)). Participants followed a 4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose. Gut metagenomes, faecal and urinary metabolites, and clinical characteristics were assessed. The dietary intervention significantly augmented faecal SCFA and increased Bifidobacteria spp., reducing PD-related gastrointestinal symptoms. The pre-existing bacterial dysbiosis in PD (depletion of Blautia, Dorea, Erysipelatoclostridium) persisted. Bacterial metabolite composition in faeces and urine positively changed with the intervention: Brain-relevant gut metabolic functions involved in neuroprotective and antioxidant pathways, including S-adenosyl methionine, glutathione, and inositol, improved in PD. These promising results warrant further investigation in larger cohorts.}, } @article {pmid40180172, year = {2025}, author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D}, title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.}, journal = {Molecular and cellular endocrinology}, volume = {603}, number = {}, pages = {112534}, doi = {10.1016/j.mce.2025.112534}, pmid = {40180172}, issn = {1872-8057}, mesh = {Humans ; Female ; *Estrogens/metabolism/blood ; Male ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Tandem Mass Spectrometry ; Chromatography, Liquid ; Young Adult ; }, abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.}, } @article {pmid40179570, year = {2025}, author = {Zhang, P and Liu, Y and Xu, M and Zhang, J and Xia, J and Shi, Y and Wang, J and Han, B and Feng, G}, title = {Gut microbiota characteristics and prognostic value in patients with aneurysmal subarachnoid hemorrhage: A clinical study.}, journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia}, volume = {136}, number = {}, pages = {111200}, doi = {10.1016/j.jocn.2025.111200}, pmid = {40179570}, issn = {1532-2653}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Subarachnoid Hemorrhage/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Prognosis ; Adult ; Aged ; Feces/microbiology ; }, abstract = {BACKGROUND: This study aims to explore the characteristics of gut microbiota in the aneurysmal subarachnoid hemorrhage (aSAH) group and the healthy control group, as well as in the good prognosis group and the poor prognosis group. It also investigates the relationship between the severity of aSAH and gut microbiota, and the predictive value of gut microbiota for the prognosis outcome of patients with aSAH.

METHODS: Stool samples from 22 patients with aSAH and 11 healthy controls were subjected to metagenomic sequencing, and species annotations were obtained through the taxonomic information database corresponding to the NR database. The characteristics of the gut microbiota in the aSAH group versus the healthy control group, and the good prognosis group versus the poor prognosis group were analyzed.The correlations between differential microbiota and clinical hematology markers between the aSAH and control groups and between gut microbiota and aSAH severity were analyzed. The prognosis of patients with aSAH after three months was assessed. Finally, gut microbiota with significant effects were screened for potential as biomarkers, and the predictive value of gut microbiota for different prognostic outcomes in patients with aSAH was explored.

RESULTS: Gut microbiota composition, diversity, and abundance differed significantly between patients in the aSAH group and the control group. Additionally, the composition, diversity, and abundance differed between patients with good and poor prognosis. Five dominant genera--Bacillus, Eggerthia, Hominisplanchenecus, Carnobacterium, and Bifidobacterium were identified as potential biomarkers for predicting aSAH outcomes.

CONCLUSION: Patients with aSAH have altered gut microbiota composition, structure, and diversity compared with the healthy population. These alterations may be potential biomarkers for aSAH diagnosis and outcome prediction.}, } @article {pmid40178790, year = {2025}, author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W}, title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).}, journal = {Science China. Life sciences}, volume = {68}, number = {6}, pages = {1541-1554}, pmid = {40178790}, issn = {1869-1889}, mesh = {China ; *Spacecraft ; *Microbiota/genetics ; Humans ; *Space Flight ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Astronauts ; }, abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.}, } @article {pmid40178526, year = {2025}, author = {Contreras-de la Rosa, PA and De la Torre-Zavala, S and O Connor-Sánchez, A and Prieto-Davó, A and Góngora-Castillo, EB}, title = {Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, pmid = {40178526}, issn = {2057-5858}, mesh = {*Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism ; Biotechnology ; Secondary Metabolism/genetics ; Metagenomics/methods ; *Geologic Sediments/microbiology ; Multigene Family ; Polyketide Synthases/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.}, } @article {pmid40178319, year = {2025}, author = {Herzog, E and Ishida, K and Scherlach, K and Chen, X and Bartels, B and Niehs, SP and Cheaib, B and Panagiotou, G and Hertweck, C}, title = {Antibacterial Siderophores of Pandoraea Pathogens and Their Impact on the Diseased Lung Microbiota.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {64}, number = {24}, pages = {e202505714}, pmid = {40178319}, issn = {1521-3773}, support = {239748522-SFB1127 ChemBioSys//Deutsche Forschungsgemeinschaft/ ; 390713860//Germany's Excellence Strategy/ ; //European Regional Development Fund/ ; //Ernst Jung Foundation/ ; }, mesh = {*Siderophores/pharmacology/chemistry/metabolism ; *Anti-Bacterial Agents/pharmacology/chemistry/metabolism ; Humans ; *Microbiota/drug effects ; *Lung/microbiology ; Microbial Sensitivity Tests ; *Burkholderiaceae/metabolism/chemistry/genetics ; Cystic Fibrosis/microbiology ; }, abstract = {Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a nonribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.}, } @article {pmid40177842, year = {2025}, author = {Larnder, AH and Manges, AR and Murphy, RA}, title = {The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.}, journal = {International journal of cancer}, volume = {157}, number = {4}, pages = {599-613}, pmid = {40177842}, issn = {1097-0215}, support = {/CAPMC/CIHR/Canada ; //Weston Family Foundation/ ; /CAPMC/CIHR/Canada ; }, mesh = {Humans ; *Breast Neoplasms/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome/physiology ; Female ; *Estrogens/metabolism ; Case-Control Studies ; }, abstract = {Increasing evidence links the gut microbiome to carcinogenesis. Disruptions in estrogen regulation by the estrobolome-gut microbiota with estrogen-related functions-may promote breast cancer. However, precise information on estrobolome targets and their underlying mechanisms is limited. This review identifies relevant targets for measuring the estrobolome, focusing on enzymes and microbial taxa involved in processing estrogens, precursors, metabolites, and phytoestrogens, to facilitate the exploration of potential links to breast cancer. Evidence from breast cancer case-control studies is synthesized to assess alignment with these targets, highlight gaps in the evidence, and suggest new paths forward. Findings from case-control studies were heterogeneous and showed limited alignment with estrobolome targets, with only Escherichia coli and Roseburia inulinivorans identified as differentially abundant and functionally relevant between cases and controls. The lack of compelling evidence for estrobolome-specific mechanisms may reflect measurement challenges or may suggest that broader ecological changes in the microbiome, which influence a network of interacting mechanisms, are more influential for carcinogenesis. To clarify the estrobolome's role in breast cancer, future research should use advanced sequencing techniques and methods such as metabolomics and transcriptomics, while considering clinical and behavioral factors that may modify estrobolome mechanisms.}, } @article {pmid40177264, year = {2025}, author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, SE and Eren, AM and Bradley, PH}, title = {Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf039}, pmid = {40177264}, issn = {2635-0041}, support = {R35 GM151155/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.

RESULTS: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism.

Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.}, } @article {pmid40176190, year = {2025}, author = {Xing, J and Niu, T and Yu, T and Zou, B and Shi, C and Wang, Y and Fan, S and Li, M and Bao, M and Sun, Y and Gao, K and Qiu, J and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, S and Hu, J and Zhang, D and Sun, W and Yang, G and Yang, W and Wang, C}, title = {Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {90}, pmid = {40176190}, issn = {2049-2618}, support = {U21A20261//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Swine ; *Porcine epidemic diarrhea virus/physiology ; *Gastrointestinal Microbiome ; *Swine Diseases/virology/microbiology ; *Faecalibacterium prausnitzii/metabolism/physiology ; *Coronavirus Infections/veterinary/virology/microbiology ; Probiotics/administration & dosage ; Feces/microbiology ; *Bacterial Outer Membrane/metabolism ; }, abstract = {BACKGROUND: The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.

RESULTS: A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.

CONCLUSION: F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.}, } @article {pmid40176137, year = {2025}, author = {Sommer, F and Bernardes, JP and Best, L and Sommer, N and Hamm, J and Messner, B and López-Agudelo, VA and Fazio, A and Marinos, G and Kadibalban, AS and Ito, G and Falk-Paulsen, M and Kaleta, C and Rosenstiel, P}, title = {Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {91}, pmid = {40176137}, issn = {2049-2618}, support = {SO1141/10-1//Deutsche Forschungsgemeinschaft/ ; CRC1182//Deutsche Forschungsgemeinschaft/ ; miTARGET//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; RNA, Ribosomal, 16S/genetics ; *Fecal Microbiota Transplantation ; *Aging/physiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; *Intestinal Mucosa/microbiology/metabolism ; *Inflammation/microbiology ; Mice, Inbred C57BL ; *Rejuvenation ; Permeability ; *Intestines/microbiology ; Metagenomics ; Intestinal Barrier Function ; }, abstract = {BACKGROUND: Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.

RESULTS: Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.

CONCLUSIONS: Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.}, } @article {pmid40175903, year = {2025}, author = {Cao, L and Sun, H and Xu, Z and Xu, X and Shi, G and Zhang, J and Liang, C and Li, T and Liu, C and Wang, M and Tian, S and Li, E}, title = {Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {190}, pmid = {40175903}, issn = {1471-2180}, mesh = {*Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; China ; Food Microbiology ; *Metagenome ; Microbiota ; *Alcoholic Beverages/microbiology ; }, abstract = {BACKGROUND: The unique flavour and quality of Baijiu, a treasure of traditional Chinese culture, has attracted increasing attention. The pit mud is a key component for forming the unique flavour styles of different Baijiu brands. Hence, conducting in-depth research on the microbial colonies present in pit mud is paramount for enhancing the intricate bouquets of Baijiu flavours.

RESULTS: This study conducts a comprehensive metagenomic examination of the microbial ecosystem within Chinese Jiang-Nong Jianxiang Baijiu fermentation pit mud. Within the pit mud walls, six prominent species, each accounting for more than 1% of the average relative abundance, emerged as key contributors: Lentilactobacillus buchneri, Secundilactobacillus silagincola, Clostridium tyrobutyricum, Lentilactobacillus parafarraginis, Ligilactobacillus acidipiscis, and Lactobacillus acetotolerans. Conversely, at the pit mud bases, four species surpassed this threshold: Petrimonas sp. IBARAKI, Methanosarcina barkeri, Methanofollis ethanolicus, and Proteiniphilum propionicum. Notably, the abundance of Clostridium in the pit mud walls impart superior saccharifying capabilities compared with those at the bases. The consistently high relative abundance of enzymes belonging to the glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) across both the pit mud walls and the bases highlight their importance in fermentation.

CONCLUSIONS: The microbial composition analysis results underscore the important role of pit mud microorganisms in facilitating starch saccharification, ethyl caproate and ethyl butyrate production, among other aromatic compounds. Microbes residing in the pit mud walls may be exhibited a heightened propensity for lactic acid generation, whereas those inhabiting the bases may be displayed a stronger inclination towards caproic acid production. This research serves as a valuable reference for future endeavours aimed at harnessing microbial resources to refine and optimize Baijiu fermentation methodologies.}, } @article {pmid40175854, year = {2025}, author = {Abuzahrah, SS}, title = {Exploring the microorganisms biodiversity associated with sponge species in the red sea through 18S ribosomal RNA gene sequencing.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {60}, pmid = {40175854}, issn = {2191-0855}, abstract = {Around the world, sponges play a significant role in marine ecosystems, and a wide variety of sponge species can be found in the coast of Red Sea of Saudi Arabia. The unique environmental conditions of the Red Sea, including warm, oligotrophic water and high salinity, have encouraged the growth of abundant sponge fauna. Our study aims to investigate the biodiversity, taxonomic composition, and phylogenetic relationships of eukaryotic organisms linked with sponges in the Red Sea off the coast of Saudi Arabia and infer the possible ecological roles and functional contributions of the identified eukaryotic taxa to sponge health and ecosystem functioning. The study investigated the microbial diversity, focusing on the genera Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and other unclassified species. Our metagenomic analysis and phylogenetic evaluation revealed a deep and diverse microbial community, with each genus performing significant ecological roles, including nutrient cycling, primary production, and contributing to marine food networks. Moreover, these genera display promising biotechnological prospects, including uses in bioremediation, biofuel production, and the synthesis of high-value biomolecules. Comparative analysis with other marine regions has focused on both the similarities and unique aspects of the Red Sea microbial community, which are influenced by its distinct environmental conditions. The gained findings contribute to a deeper understanding of the ecological dynamics in the Red Sea and open new avenues for biotechnological exploration in marine ecosystems.}, } @article {pmid40175737, year = {2025}, author = {Sawhney, SS and Thänert, R and Thänert, A and Hall-Moore, C and Ndao, IM and Mahmud, B and Warner, BB and Tarr, PI and Dantas, G}, title = {Gut microbiome evolution from infancy to 8 years of age.}, journal = {Nature medicine}, volume = {31}, number = {6}, pages = {2004-2015}, pmid = {40175737}, issn = {1546-170X}, support = {R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; 5P30 DK052574//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01AI155893//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 HD092414/HD/NICHD NIH HHS/United States ; T32GM007067//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 AI155893/AI/NIAID NIH HHS/United States ; MD-FR-2013-292//Children's Discovery Institute (CDI)/ ; T32 GM007067/GM/NIGMS NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Feces/microbiology ; Child ; Child, Preschool ; Male ; Infant, Newborn ; Metagenome/genetics ; Bacteria/genetics/classification ; }, abstract = {The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.}, } @article {pmid40175647, year = {2025}, author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ}, title = {Increasing spatial working memory in mice with Akkermansia muciniphila.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {546}, pmid = {40175647}, issn = {2399-3642}, support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; *Memory, Short-Term/physiology ; Male ; *Spatial Memory/physiology ; Akkermansia ; Humans ; Verrucomicrobia ; Feces/microbiology ; Brain-Derived Neurotrophic Factor/metabolism ; }, abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.}, } @article {pmid40175554, year = {2025}, author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ}, title = {Bifidobacteria support optimal infant vaccine responses.}, journal = {Nature}, volume = {641}, number = {8062}, pages = {456-464}, pmid = {40175554}, issn = {1476-4687}, mesh = {*Bifidobacterium/immunology/physiology/drug effects/isolation & purification ; Mice ; Infant ; Animals ; Humans ; Female ; *Pneumococcal Vaccines/immunology ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Feces/microbiology ; Male ; Haemophilus Vaccines/immunology ; *Immunogenicity, Vaccine/immunology/drug effects ; Gastrointestinal Microbiome/drug effects/immunology ; Germ-Free Life ; Prospective Studies ; Probiotics/administration & dosage ; Vaccines, Conjugate/immunology ; Vaccination ; Antibodies, Bacterial/immunology ; }, abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.}, } @article {pmid40175313, year = {2025}, author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B}, title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: a metagenomic perspective.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40175313}, issn = {1574-6941}, support = {//Virginia Water Resources Research Center/ ; 1737258//National Science Foundation/ ; }, mesh = {*Biofilms/growth & development ; *Microplastics/metabolism ; Biodegradation, Environmental ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification ; Metagenomics ; *Plastics/metabolism ; Metagenome ; Nitrification ; Microbiota ; Water Pollutants, Chemical/metabolism ; Petroleum/metabolism ; Polyesters ; }, abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome-assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic-degrading capabilities.}, } @article {pmid40174744, year = {2025}, author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W}, title = {Thermal environment driving specific microbial species to form the visible biofilms on the UNESCO World Heritage Dazu Rock Carvings.}, journal = {Environmental research}, volume = {276}, number = {}, pages = {121510}, doi = {10.1016/j.envres.2025.121510}, pmid = {40174744}, issn = {1096-0953}, mesh = {*Biofilms/growth & development ; Bacteria/classification ; Fungi ; *Microbiota ; Temperature ; }, abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4 °C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.}, } @article {pmid40174574, year = {2025}, author = {Zeng, S and Almeida, A and Mu, D and Wang, S}, title = {Embracing the unknown: Proteomic insights into the human microbiome.}, journal = {Cell metabolism}, volume = {37}, number = {4}, pages = {799-801}, doi = {10.1016/j.cmet.2025.02.003}, pmid = {40174574}, issn = {1932-7420}, mesh = {Humans ; *Proteomics/methods ; *Microbiota ; Animals ; *Gastrointestinal Microbiome ; Mice ; Inflammatory Bowel Diseases/microbiology/metabolism ; Metagenome ; *Proteome ; }, abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.}, } @article {pmid40172536, year = {2025}, author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR}, title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.}, journal = {Infection and immunity}, volume = {93}, number = {5}, pages = {e0056924}, pmid = {40172536}, issn = {1098-5522}, support = {IOS-2131060//National Science Foundation/ ; IOS-2131061//National Science Foundation/ ; BB/W013517/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Skin/microbiology/immunology ; *Xenopus laevis/microbiology/immunology/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Batrachochytrium ; Transcriptome ; }, abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.}, } @article {pmid40172215, year = {2025}, author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F}, title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2486511}, pmid = {40172215}, issn = {1949-0984}, support = {R01 DK126969/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/metabolism/pathology/virology ; Metagenomics ; Disease Models, Animal ; Metabolomics ; *Aging/metabolism ; SARS-CoV-2 ; Cricetinae ; Male ; Dysbiosis/microbiology ; Age Factors ; Metabolome ; Bacteria/classification/genetics/metabolism/isolation & purification ; Mesocricetus ; Lung/pathology ; }, abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.}, } @article {pmid40172109, year = {2025}, author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M}, title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {89}, number = {2}, pages = {e0018423}, pmid = {40172109}, issn = {1098-5557}, support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 16/SP/3827/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Vitamins/biosynthesis ; *Bacteria/metabolism/genetics ; *Gastrointestinal Tract/microbiology/metabolism ; Mammals/microbiology ; *Host Microbial Interactions ; }, abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.}, } @article {pmid40171165, year = {2025}, author = {Shi, H and Li, J}, title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1485048}, pmid = {40171165}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Obesity/microbiology/surgery ; *Bariatric Surgery ; Metagenomics/methods ; *Metagenome ; *Bacteria/genetics/classification ; Female ; Male ; Computational Biology ; Genomics ; Adult ; Middle Aged ; }, abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.

METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota α-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).

RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota α-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.

DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.}, } @article {pmid40170844, year = {2025}, author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J}, title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1539653}, pmid = {40170844}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Metagenomics/methods ; *Melanoma/therapy/immunology/microbiology ; *Machine Learning ; *Immunotherapy/methods ; Female ; Male ; *Bacteria/genetics ; *Fungi/genetics ; Middle Aged ; Feces/microbiology ; Biomarkers ; *Skin Neoplasms/therapy/microbiology/immunology ; Aged ; Treatment Outcome ; }, abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.

METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.

RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.

CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.}, } @article {pmid40170447, year = {2025}, author = {Veríssimo, J and Lopes-Lima, M and Amaral, F and Chaves, C and Fernandes, V and Kemanja, M and Teixeira, A and Martins, FMS and Beja, P}, title = {Navigating Methodological Trade-Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14082}, pmid = {40170447}, issn = {1755-0998}, support = {2020.03608.CEECIND//Fundação para a Ciência e a Tecnologia/ ; COVID/BD/152600/2022//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/133159/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund (ERDF)/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; *Metagenomics/methods ; Mediterranean Region ; *Vertebrates/classification/genetics ; *Environmental Monitoring/methods ; }, abstract = {Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high- versus low-capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high-capacity filtration and sampling across multiple sites. Site-level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site-level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade-offs in different study systems.}, } @article {pmid40170118, year = {2025}, author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P}, title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {89}, pmid = {40170118}, issn = {2049-2618}, support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; }, mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/metabolism/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide/metabolism ; Temperature ; Microbiota ; Carbon Isotopes ; Metagenomics ; Benzaldehydes/metabolism ; Carbon Cycle ; }, abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.}, } @article {pmid40169660, year = {2025}, author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE}, title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {547}, pmid = {40169660}, issn = {2052-4463}, mesh = {Animals ; *Cattle/microbiology ; Feces/microbiology ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.}, } @article {pmid40169555, year = {2025}, author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P}, title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {115}, pmid = {40169555}, issn = {2158-3188}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Feces/chemistry/microbiology ; Mice ; *Metabolome ; *Stress, Psychological/metabolism/microbiology ; Male ; *Social Defeat ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal/physiology ; Disease Models, Animal ; Humans ; *Depression/metabolism/microbiology ; Anhedonia/physiology ; Female ; Mice, Inbred C57BL ; }, abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.}, } @article {pmid40169141, year = {2025}, author = {Zhang, J and Ying, X and Hu, R and Huang, Y and Wang, R and Wu, L and Han, D and Ma, R and He, K}, title = {Metagenomic and metabolomic analysis of gut microbiome's role in spinal cord injury recovery in rats.}, journal = {Biomolecules & biomedicine}, volume = {25}, number = {9}, pages = {2114-2126}, doi = {10.17305/bb.2025.12164}, pmid = {40169141}, issn = {2831-090X}, mesh = {Animals ; *Spinal Cord Injuries/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Rats ; Rats, Sprague-Dawley ; Male ; *Metabolomics/methods ; *Metagenomics/methods ; Feces/microbiology ; Metabolome ; }, abstract = {Spinal cord injury (SCI) induces profound systemic changes, including disruptions in gut microbiome composition and host metabolism. This study aimed to investigate the impact of SCI on gut microbial diversity and serum metabolites in rats, and to explore potential microbiome-metabolite interactions that may influence recovery. Male Sprague-Dawley (SD) rats were assigned to either SCI or sham-operated groups. Fecal samples were collected for whole-genome metagenomic sequencing, and serum samples were analyzed using untargeted metabolomics. Gut microbial composition and diversity were assessed using α- and β-diversity indices, while Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa. Metabolomic pathway analysis was performed to detect significant changes in serum metabolites, and Spearman's correlation was used to evaluate associations between gut microbes and metabolites. SCI significantly altered gut microbiota composition, with increased proportions of Ligilactobacillus and Staphylococcus, and decreased proportions of Lactobacillus and Limosilactobacillus. Metabolomic analysis revealed disrupted energy metabolism and elevated oxidative stress in SCI rats, as indicated by increased serum levels of pyruvate and lactic acid. Correlation analysis further identified significant associations between specific gut bacteria and key metabolites, suggesting microbiome-driven metabolic dysregulation following SCI. These findings highlight significant interactions between the gut microbiota and host metabolism after SCI and suggest that microbiome-targeted interventions may hold therapeutic potential for improving recovery by modulating metabolic function and oxidative stress responses.}, } @article {pmid40169018, year = {2025}, author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B}, title = {Making sense of the virome in light of evolution and ecology.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2044}, pages = {20250389}, pmid = {40169018}, issn = {1471-2954}, support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*Virome ; *Biological Evolution ; *Viruses/genetics ; Ecosystem ; Ecology ; }, abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.}, } @article {pmid40168930, year = {2025}, author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY}, title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138077}, doi = {10.1016/j.jhazmat.2025.138077}, pmid = {40168930}, issn = {1873-3336}, mesh = {*Rhizosphere ; *Lactuca/genetics/microbiology/metabolism ; Genotype ; *Soil Pollutants/metabolism ; *Bacteria/genetics/metabolism ; Soil Microbiology ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology/metabolism ; *Diethylhexyl Phthalate/metabolism ; *Phthalic Acids/metabolism ; Microbiota ; }, abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.}, } @article {pmid40168325, year = {2025}, author = {Yun, H and Seo, JH and Kim, YK and Yang, J}, title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320916}, pmid = {40168325}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Extracellular Vesicles/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Air Microbiology ; Microbiota ; Metagenomics ; Republic of Korea ; }, abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.}, } @article {pmid40167332, year = {2025}, author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF}, title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14105}, pmid = {40167332}, issn = {1755-0998}, support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; }, mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Metagenome ; }, abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.}, } @article {pmid40165946, year = {2025}, author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X}, title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1563225}, pmid = {40165946}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Zingiber officinale/chemistry ; Male ; *Enteritis/drug therapy/microbiology/metabolism/pathology ; Powders ; *Pomegranate/chemistry ; Disease Models, Animal ; Female ; Chronic Disease ; *Plant Extracts/pharmacology ; Cytokines/blood ; }, abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.}, } @article {pmid40165255, year = {2025}, author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J}, title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {141}, pmid = {40165255}, issn = {1466-609X}, support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Prospective Studies ; Middle Aged ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/analysis ; Cohort Studies ; }, abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.

METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.

RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.

CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.}, } @article {pmid40164980, year = {2025}, author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM}, title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2484385}, pmid = {40164980}, issn = {1949-0984}, mesh = {Animals ; *Hominidae/microbiology/physiology ; *Diet ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Life Style ; *Gastrointestinal Microbiome/genetics ; Pan troglodytes/microbiology ; Adaptation, Physiological ; Africa ; Phylogeny ; Metagenome ; }, abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.}, } @article {pmid40164860, year = {2025}, author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG}, title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.}, journal = {Tropical animal health and production}, volume = {57}, number = {3}, pages = {148}, pmid = {40164860}, issn = {1573-7438}, mesh = {Animals ; *Probiotics/administration & dosage ; Cattle/microbiology/metabolism ; *Rumen/microbiology/metabolism ; *Amino Acids/administration & dosage/metabolism ; *Metabolome/drug effects ; *Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; Animal Feed/analysis ; Male ; Cross-Over Studies ; Bacteria/classification/isolation & purification ; Animal Nutritional Physiological Phenomena ; }, abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.}, } @article {pmid40164832, year = {2025}, author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA}, title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.}, journal = {Nature microbiology}, volume = {10}, number = {5}, pages = {1240-1257}, pmid = {40164832}, issn = {2058-5276}, support = {DP1 DK140021/DK/NIDDK NIH HHS/United States ; R01 DK129691/DK/NIDDK NIH HHS/United States ; R01 EY031209/EY/NEI NIH HHS/United States ; R01 EY030192/EY/NEI NIH HHS/United States ; DP2 AG067492/AG/NIA NIH HHS/United States ; R01 NS134976/NS/NINDS NIH HHS/United States ; P30 AG038070/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 HL113147/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Aging/genetics/physiology ; *Gastrointestinal Microbiome/genetics ; Mice ; *Caloric Restriction ; *Metagenome ; Humans ; Male ; Mice, Inbred C57BL ; Female ; Longevity ; }, abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.}, } @article {pmid40164697, year = {2025}, author = {Jia, L and Ke, Y and Zhao, S and Liu, J and Luo, X and Cao, J and Liu, Y and Guo, Q and Chen, WH and Chen, F and , and Wang, J and Wu, H and Ding, J and Zhao, XM}, title = {Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease.}, journal = {Molecular psychiatry}, volume = {30}, number = {9}, pages = {3951-3962}, pmid = {40164697}, issn = {1476-5578}, mesh = {*Gastrointestinal Microbiome/genetics/physiology ; *Alzheimer Disease/microbiology/genetics/metabolism ; Humans ; Metagenomics/methods ; Male ; Female ; Mice ; Animals ; Aged ; Feces/microbiology ; Dysbiosis/microbiology/genetics ; Disease Progression ; Cohort Studies ; Fecal Microbiota Transplantation/methods ; Metagenome/genetics ; Brain/metabolism ; Middle Aged ; Cognitive Dysfunction/microbiology ; }, abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.}, } @article {pmid40164638, year = {2025}, author = {Mills, S and Ijaz, UZ and Lens, PNL}, title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {54}, pmid = {40164638}, issn = {2055-5008}, support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Microbial Consortia ; Metagenome ; High-Throughput Nucleotide Sequencing ; Methane/metabolism ; }, abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.}, } @article {pmid40162572, year = {2025}, author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y}, title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {23}, pages = {e2502743}, pmid = {40162572}, issn = {2198-3844}, support = {2024YFD1700500//National Key R&D Program of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&D Program of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&F University Young Talent Project/ ; }, mesh = {*Ammonia/metabolism ; *Methane/metabolism ; *Archaea/metabolism ; *Bacteria/metabolism ; Hydrogen/metabolism ; Anaerobiosis ; Microbiota ; }, abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.}, } @article {pmid40158829, year = {2025}, author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G}, title = {Huang-qin decoction alleviates deoxycholic acid-induced colorectal cancer in mice by regulating gut microbiota.}, journal = {Journal of ethnopharmacology}, volume = {346}, number = {}, pages = {119715}, doi = {10.1016/j.jep.2025.119715}, pmid = {40158829}, issn = {1872-7573}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/chemically induced/drug therapy/microbiology/pathology ; Mice ; Deoxycholic Acid/toxicity ; Male ; Mice, Inbred C57BL ; Protein Interaction Maps/drug effects ; Network Pharmacology ; Apoptosis/drug effects ; Astragalus propinquus ; }, abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.

AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.

METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2 % deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.

RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.

CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.}, } @article {pmid40158160, year = {2025}, author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J}, title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {50}, pmid = {40158160}, issn = {1475-2891}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Child, Preschool ; Male ; Child ; Female ; Cross-Sectional Studies ; *Metabolome/physiology ; *Diet ; China ; Feces/microbiology ; *Metabolomics/methods ; *Nutritional Status ; Metagenomics ; Multiomics ; }, abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.}, } @article {pmid40158141, year = {2025}, author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY}, title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {87}, pmid = {40158141}, issn = {2049-2618}, support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; }, mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Computer Simulation ; }, abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.}, } @article {pmid40157594, year = {2025}, author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D}, title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {200}, number = {}, pages = {115419}, doi = {10.1016/j.fct.2025.115419}, pmid = {40157594}, issn = {1873-6351}, mesh = {Animals ; *Zea mays/genetics/metabolism ; *Plants, Genetically Modified/genetics/metabolism ; *Gastrointestinal Microbiome/drug effects ; Macaca fascicularis ; *Endotoxins/genetics/metabolism ; *Hemolysin Proteins/genetics/metabolism ; Bacillus thuringiensis Toxins ; *Animal Feed/analysis ; Male ; *Bacterial Proteins/genetics/metabolism ; Female ; }, abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70 % non-GM maize (Corn group), and diet formulation containing 70 % GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.}, } @article {pmid40157532, year = {2025}, author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA}, title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).}, journal = {Journal of invertebrate pathology}, volume = {211}, number = {}, pages = {108322}, doi = {10.1016/j.jip.2025.108322}, pmid = {40157532}, issn = {1096-0805}, mesh = {Animals ; *Diptera/virology ; *Insect Viruses/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays ; *Virome ; }, abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.}, } @article {pmid40156868, year = {2025}, author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L}, title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.}, journal = {Nucleic acids research}, volume = {53}, number = {6}, pages = {}, pmid = {40156868}, issn = {1362-4962}, support = {R44 AI172703/AI/NIAID NIH HHS/United States ; //Bill & Melinda Gates Foundation/ ; //New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; }, mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Substrate Specificity ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/enzymology ; Bacteriophages/genetics ; }, abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.}, } @article {pmid40156579, year = {2025}, author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D}, title = {Revealing microbial functionalities and ecological roles in Rajpardi lignite mine: insights from metagenomics analysis.}, journal = {Letters in applied microbiology}, volume = {78}, number = {4}, pages = {}, doi = {10.1093/lambio/ovaf048}, pmid = {40156579}, issn = {1472-765X}, mesh = {*Metagenomics ; India ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Mining ; *Soil Microbiology ; Phylogeny ; *Microbiota ; }, abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10 071 318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasizing the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.}, } @article {pmid40156577, year = {2025}, author = {Kop, LFM and Koch, H and Dalcin Martins, P and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S}, title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40156577}, issn = {1574-6941}, support = {2022-06725//Swedish Research Council/ ; 024.002.002/NWO_/Dutch Research Council/Netherlands ; //Norwegian Public Roads Administration/ ; }, mesh = {*Biofilms/growth & development ; *Nitrification ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Archaea/genetics/classification/isolation & purification/metabolism ; Norway ; Phylogeny ; *Biodiversity ; Metagenomics ; Construction Materials/microbiology ; }, abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7 ± 15% but a wide range between 1.2% and 61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.}, } @article {pmid40156536, year = {2025}, author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ}, title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.}, journal = {Australian veterinary journal}, volume = {103}, number = {7}, pages = {416-421}, pmid = {40156536}, issn = {1751-0813}, support = {DE200100367//Australian Research Council/ ; }, mesh = {Animals ; *Circovirus/genetics/isolation & purification ; *Genome, Viral ; *Bird Diseases/virology ; Phylogeny ; *Circoviridae Infections/veterinary/virology ; *Parakeets/virology ; *Parvovirus/genetics/isolation & purification ; Endangered Species ; Feces/virology ; *Parvoviridae Infections/veterinary/virology ; }, abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.}, } @article {pmid40154057, year = {2025}, author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y}, title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.}, journal = {Food chemistry}, volume = {481}, number = {}, pages = {143980}, doi = {10.1016/j.foodchem.2025.143980}, pmid = {40154057}, issn = {1873-7072}, mesh = {Fermentation ; *Microbiota ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metabolomics ; }, abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.}, } @article {pmid40153355, year = {2025}, author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T}, title = {Bacterial consortia of ewes' whey in the production of bryndza cheese in Slovakia.}, journal = {Letters in applied microbiology}, volume = {78}, number = {4}, pages = {}, doi = {10.1093/lambio/ovaf047}, pmid = {40153355}, issn = {1472-765X}, support = {APVV-20-0001//Slovak Research and Development Agency/ ; }, mesh = {Animals ; Slovakia ; *Cheese/microbiology ; *Whey/microbiology ; Sheep ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/classification/genetics/isolation & purification ; *Microbial Consortia ; Female ; Food Microbiology ; DNA, Bacterial/genetics/chemistry ; Milk/microbiology ; }, abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characteristics of the final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes' milk-based bryndza cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3-8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, L. diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, L. delbrueckii, L. gasseri and L. otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase-positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.}, } @article {pmid40152095, year = {2025}, author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q}, title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.}, journal = {Food & function}, volume = {16}, number = {8}, pages = {3101-3119}, doi = {10.1039/d4fo06308b}, pmid = {40152095}, issn = {2042-650X}, mesh = {Cell Line, Tumor ; Humans ; *Signal Transduction ; Lactic Acid/metabolism ; NF-kappa B/metabolism ; *Gastritis/metabolism/microbiology/pathology ; *Lactobacillaceae/physiology ; Helicobacter pylori ; *Helicobacter Infections/metabolism/microbiology/pathology ; Animals ; Mice ; Mice, Inbred C57BL ; Sulfones/pharmacology ; Nitriles/pharmacology ; Gastrointestinal Microbiome ; }, abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.}, } @article {pmid40151093, year = {2025}, author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J}, title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.}, journal = {Journal of basic microbiology}, volume = {65}, number = {7}, pages = {e70024}, doi = {10.1002/jobm.70024}, pmid = {40151093}, issn = {1521-4028}, support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; }, mesh = {*Quorum Sensing/physiology ; *Homoserine/analogs & derivatives/metabolism ; *Lactones/metabolism ; Humans ; *Signal Transduction ; Bacterial Proteins/metabolism/genetics ; *Bacteria/metabolism/genetics/classification ; Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.}, } @article {pmid40150979, year = {2025}, author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN}, title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {17}, number = {1}, pages = {25725}, doi = {10.31083/FBE25725}, pmid = {40150979}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Endometrium/microbiology/metabolism ; *Rectum/microbiology ; *Metabolic Networks and Pathways ; *Microbiota ; Metagenomics ; Diet/veterinary ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.

METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.

RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).

CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.}, } @article {pmid40149936, year = {2025}, author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C}, title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {3}, pages = {}, pmid = {40149936}, issn = {2218-273X}, mesh = {*Berberine/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; *Colitis, Ulcerative/drug therapy/microbiology ; Bacteria/genetics/drug effects ; Male ; }, abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.}, } @article {pmid40149437, year = {2025}, author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A}, title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, pmid = {40149437}, issn = {2073-4425}, mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics ; Metagenomics/methods ; Bacteria/genetics/classification ; Soil/chemistry ; Ecosystem ; Plant Roots/microbiology ; Metagenome ; Microbiota ; }, abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.}, } @article {pmid40148567, year = {2025}, author = {Austin, GI and Brown Kav, A and ElNaggar, S and Park, H and Biermann, J and Uhlemann, AC and Pe'er, I and Korem, T}, title = {Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.}, journal = {Nature microbiology}, volume = {10}, number = {4}, pages = {897-911}, pmid = {40148567}, issn = {2058-5276}, support = {R01HD114715//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T15 LM007079/LM/NLM NIH HHS/United States ; R01HD106017//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01 HD114715/HD/NICHD NIH HHS/United States ; U54DK104309//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; T15LM007079//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; U54 DK104309/DK/NIDDK NIH HHS/United States ; R01 HD106017/HD/NICHD NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Humans ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Computational Biology/methods ; Bias ; }, abstract = {Every step in common microbiome profiling protocols has variable efficiency for each microbe, for example, different DNA extraction efficiency for Gram-positive bacteria. These processing biases impede the identification of signals that are biologically interpretable and generalizable across studies. 'Batch-correction' methods have been used to address these issues computationally with some success, but they are largely non-interpretable and often require the use of an outcome variable in a manner that risks overfitting. We present DEBIAS-M (domain adaptation with phenotype estimation and batch integration across studies of the microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using diverse benchmarks including 16S rRNA and metagenomic sequencing, classification and regression, and a variety of clinical and molecular targets, we demonstrate that using DEBIAS-M improves cross-study prediction accuracy compared with commonly used batch-correction methods. Notably, we show that the inferred bias-correction factors are stable, interpretable and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M facilitates improved modelling of microbiome data and identification of interpretable signals that generalize across studies.}, } @article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; }, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, } @article {pmid40147232, year = {2025}, author = {Wang, J and Ge, Y}, title = {Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content.}, journal = {The Science of the total environment}, volume = {974}, number = {}, pages = {179224}, doi = {10.1016/j.scitotenv.2025.179224}, pmid = {40147232}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metagenome ; Soil/chemistry ; Bacteria/genetics ; Microbiota ; }, abstract = {Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.}, } @article {pmid40146796, year = {2025}, author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S}, title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.}, journal = {Polish journal of microbiology}, volume = {74}, number = {1}, pages = {71-81}, pmid = {40146796}, issn = {2544-4646}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Aged ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Case-Control Studies ; }, abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.}, } @article {pmid40145240, year = {2025}, author = {Zhou, Y and Oba, K and Xu, T and Kuroiwa, M and Hori, T and Terada, A}, title = {Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol.}, journal = {Environmental science & technology}, volume = {59}, number = {13}, pages = {6673-6685}, doi = {10.1021/acs.est.4c12732}, pmid = {40145240}, issn = {1520-5851}, mesh = {Methanol/metabolism ; *Nitrous Oxide/metabolism ; Oxygen/metabolism ; *Microbial Consortia ; Bacteria/metabolism ; Oxidation-Reduction ; }, abstract = {Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. [15]N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass[-1]·h[-1]. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min[-1]) and low (0.08 mmol·min[-1]) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.}, } @article {pmid40144403, year = {2025}, author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X}, title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf042}, pmid = {40144403}, issn = {2730-6151}, abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.}, } @article {pmid40142589, year = {2025}, author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M}, title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, pmid = {40142589}, issn = {2076-2607}, support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; }, abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.}, } @article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, } @article {pmid40140988, year = {2025}, author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W}, title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {30}, pmid = {40140988}, issn = {1756-994X}, mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome/genetics ; Male ; *Viruses/genetics/classification ; Female ; Metagenome ; Feces/virology ; China ; Genome, Viral ; Adult ; Middle Aged ; Metagenomics/methods ; East Asian People ; }, abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.}, } @article {pmid40140706, year = {2025}, author = {Best, L and Dost, T and Esser, D and Flor, S and Gamarra, AM and Haase, M and Kadibalban, AS and Marinos, G and Walker, A and Zimmermann, J and Simon, R and Schmidt, S and Taubenheim, J and Künzel, S and Häsler, R and Franzenburg, S and Groth, M and Waschina, S and Rosenstiel, P and Sommer, F and Witte, OW and Schmitt-Kopplin, P and Baines, JF and Frahm, C and Kaleta, C}, title = {Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.}, journal = {Nature microbiology}, volume = {10}, number = {4}, pages = {973-991}, pmid = {40140706}, issn = {2058-5276}, support = {859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; FOR5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 416 418087534//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; Mice ; *Aging/metabolism ; *Gastrointestinal Microbiome/physiology ; Metabolomics ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Mice, Inbred C57BL ; Metagenomics ; Male ; }, abstract = {Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice with metabolic modelling to characterize host-microbiome interactions during aging. Reconstructing integrated metabolic models of host and 181 mouse gut microorganisms, we show a complex dependency of host metabolism on known and previously undescribed microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These changes coincided with increased systemic inflammation and the downregulation of essential host pathways, particularly in nucleotide metabolism, predicted to rely on the microbiota and critical for preserving intestinal barrier function, cellular replication and homeostasis. Our results elucidate microbiome-host interactions that potentially influence host aging processes. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies.}, } @article {pmid40140705, year = {2025}, author = {Garrido-Sanz, D and Keel, C}, title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.}, journal = {Nature microbiology}, volume = {10}, number = {5}, pages = {1130-1144}, pmid = {40140705}, issn = {2058-5276}, mesh = {*Triticum/microbiology ; *Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; *Seeds/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Plant Roots/microbiology ; }, abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.}, } @article {pmid40140473, year = {2025}, author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA}, title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10378}, pmid = {40140473}, issn = {2045-2322}, mesh = {Humans ; Adolescent ; *Gastrointestinal Microbiome ; Male ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism/microbiology ; Biomarkers/metabolism ; *Attention Deficit Disorder with Hyperactivity/microbiology ; Depression/microbiology ; Anxiety/microbiology ; *Mental Health ; Feces/microbiology ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.}, } @article {pmid40139249, year = {2025}, author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL}, title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.}, journal = {Journal of wildlife diseases}, volume = {61}, number = {2}, pages = {382-395}, doi = {10.7589/JWD-D-24-00115}, pmid = {40139249}, issn = {1943-3700}, mesh = {Animals ; *Nematoda/isolation & purification/genetics ; Metagenomics ; *Bird Diseases/parasitology/virology ; *Nematode Infections/veterinary/parasitology ; *Viruses/isolation & purification/classification ; Female ; Male ; }, abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.}, } @article {pmid40138872, year = {2025}, author = {Liang, T and Jiang, T and Liang, Z and Li, L and Chen, Y and Chen, T and Yang, L and Zhang, N and Dong, B and Xie, X and Gu, B and Wu, Q}, title = {Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128145}, doi = {10.1016/j.micres.2025.128145}, pmid = {40138872}, issn = {1618-0623}, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Staphylococcus aureus/enzymology/genetics/metabolism ; *Amino Acids, Branched-Chain/biosynthesis ; *Acetolactate Synthase/metabolism/genetics ; Humans ; Animals ; Mice ; China ; Male ; Insulin Resistance ; Female ; Middle Aged ; *Glycemic Control ; Blood Glucose ; Feces/microbiology ; Staphylococcal Infections/microbiology ; Metagenomics ; Prediabetic State/microbiology ; Metabolomics ; Insulin ; }, abstract = {An increase in branched-chain amino acid (BCAA) levels can result in insulin resistance at different stages of type 2 diabetes (T2D), however, the causes of this increase are unclear. We performed metagenomics and metabolomics profiling in patients with prediabetes (PDM), newly diagnosed diabetes (NDDM), and post-medication type 2 diabetes (P2DM) to investigate whether altered gut microbes and metabolites could explain the specific clinical characteristics of different disease stages of T2D. Here we identify acetolactate synthase (ALS) a BCAA biosynthesis enzyme in Staphylococcus aureus as a cause of T2D insulin resistance. Compared with healthy peoples, patients with PDM, NDDM, and P2DM groups, especially in P2DM group, have increased faecal numbers of S. aureus. We also demonstrated that insulin administration may be a risk factor for S. aureus infection in T2D. The presence of ALS-positive S. aureus correlated with the levels of BCAAs and was associated with an increased fasting blood glucose (FBG) and insulin resistance. Humanized microbiota transplantation experiment indicated that ALS contributes to disordered insulin resistance mediated by S. aureus. We also found that S. aureus phage can reduced the FBG levels and insulin resistance in db/db mice. The ALS-positive S. aureus are associated with insulin resistance in T2D, opening a new therapeutic avenue for the prevention or treatment of diabetes.}, } @article {pmid40138008, year = {2025}, author = {Davasaz Tabrizi, E and Sevil, M and Arican, E}, title = {Bioinformatic strategies in metagenomics of chronic prostatitis.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {188}, pmid = {40138008}, issn = {1433-8726}, mesh = {Male ; Humans ; *Prostatitis/microbiology/urine ; Adult ; *Computational Biology/methods ; *Metagenomics/methods ; Chronic Disease ; *Microbiota ; Middle Aged ; Young Adult ; Case-Control Studies ; Virulence Factors/genetics ; }, abstract = {PURPOSE: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent urological condition in young men, significantly affecting quality of life due to persistent discomfort and neuropsychological symptoms. Despite its high prevalence, the etiology of CP/CPPS remains poorly understood. This study investigated urinary microbiota differences between CP/CPPS patients and healthy controls to identify microbial contributors, antibiotic resistance genes (ARGs), and virulence factors of dominant bacteria, as well as to explore potential therapeutic targets.

METHODS: Urine samples were collected from 58 CP/CPPS patients and 25 controls. Symptom severity was assessed by a specialist urologist using the NIH Chronic Prostatitis Symptom Index and UPOINT classification. Bacterial-specific 16 S rRNA sequencing was performed using nanopore technology, with bioinformatics analyses conducted via ONT guppy 5.0.11, NCBI and SLV 16 S bacterial taxonomic databases, UPGMA hierarchical clustering, and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pairwise comparisons were analyzed using the Mann-Whitney U test.

RESULTS: Distinct microbial diversity patterns were observed between patients and controls. Bacillus species were significantly enriched in CP/CPPS patients, while Enterococcus species predominated in controls. Younger patients exhibited unique microbiome profiles compared to older groups. Bioinformatics analyses identified ARGs and virulence factors associated with Bacillus species, implicating them in localized inflammation. Antibiotics like pleuromutilin or vancomycin were identified as potential therapeutic options, though experimental validation was beyond the study's scope.

CONCLUSION: These findings highlight microbial imbalances and provide a foundation for microbiome-targeted therapeutic strategies for CP/CPPS management in the future. Additionally, the identification of bacterial virulence factors and ARG provides insights into the potential mechanisms driving persistent symptoms. Future research with larger cohorts and experimental validation of the suggested therapeutic options may contribute to more effective treatment for CP/CPPS.}, } @article {pmid40137713, year = {2025}, author = {Shaw, CA and Soltero-Rivera, M and Profeta, R and Weimer, BC}, title = {Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, pmid = {40137713}, issn = {2076-0817}, support = {UL1 TR001860/NH/NIH HHS/United States ; }, mesh = {Animals ; Cats ; *Microbiota/genetics ; *Cat Diseases/microbiology/pathology ; *Stomatitis/microbiology/veterinary/pathology ; *Aggressive Periodontitis/microbiology/veterinary/pathology ; Male ; Disease Progression ; Mouth/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {Aggressive Periodontitis (AP) and Feline Chronic Gingivostomatitis (FCGS) are two oral inflammatory diseases in cats with unknown etiology. Both conditions present with severe inflammation of the oral cavity and in FCGS it is found with additional deterioration of the non-keratinized mucosa. The oral microbiome is increasingly implicated in disease progression, but little is known about shifts in the microbial community during the AP and FCGS progression. To that end, we used deep metagenomic sequencing with total RNA on three longitudinal samples of the oral microbiome in a cat first diagnosed with AP that progressed to FCGS. This deep sequencing approach revealed that increased diversity at both the genus and species levels marked the shift from AP to FCGS, including increases in Porphyromonas and Treponema species, and decreased Streptobacillus species. The metatranscriptomes were then probed for expression of antimicrobial resistance genes and virulence factors. Disease-related genes that include cheY, and ompP5 were expressed in early AP and FCGS, while others like galU were only expressed in one or the other disease state. Both genus and species-level shifts were observed along the longitudinal microbiome samples with a noted increase in species diversity in the FCGS-associated microbiome. Corroborating that functional shifts accompany taxonomic changes, the AMR and virulence factor expression similarly changed between the sampling points. Together, these taxonomic and functional shifts indicate that AP and FCGS are potentially linked and may be marked by changes in the oral microbiome, which supports the development of microbial-based clinical diagnostics and therapeutics.}, } @article {pmid40136549, year = {2025}, author = {Pizzi, S and Conti, A and Di Canito, A and Casagrande Pierantoni, D and Foschino, R and Setati, ME and Vigentini, I}, title = {Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136549}, issn = {2079-7737}, support = {150549//Italy/South Africa Joint Research Programme (ISARP) 2023-2025/ ; }, abstract = {This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.}, } @article {pmid40135776, year = {2025}, author = {Wang, J and Liu, Q and Jin, S and Yang, B and Wang, C and Tan, Y and Feng, W and Tao, J and Wang, H and Wang, Y and Yang, S and Cui, L}, title = {Characterization of Bile Microbiota in Patients With Obstructive Jaundice Associated With Biliary Tract Diseases.}, journal = {Clinical and translational gastroenterology}, volume = {16}, number = {7}, pages = {e00841}, pmid = {40135776}, issn = {2155-384X}, support = {62071011，81800604, 2023YFC2413802//National Natural Science Foundation of China, Key Clinical Specialty Funding Project of Beijin, Hospital-Enterprise Joint Funding Project, National Key Research and Development Program/ ; }, mesh = {Humans ; *Jaundice, Obstructive/microbiology/diagnosis/etiology ; Male ; *Bile/microbiology/chemistry ; Female ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; *Gallstones/microbiology/complications ; *Microbiota/genetics ; *Bacteria/isolation & purification/genetics/classification ; Metagenomics ; *Cholangiocarcinoma/microbiology/complications/diagnosis ; Biomarkers/analysis ; *Bile Duct Neoplasms/microbiology/complications/diagnosis ; Adult ; High-Throughput Nucleotide Sequencing ; Constriction, Pathologic/microbiology ; }, abstract = {INTRODUCTION: Cholangiocarcinoma (CHOL), a malignant tumor of the biliary system, is particularly concerning because of its high malignancy and poor prognosis, often leading to obstructive jaundice. The advent of metagenomic next-generation sequencing technology has expanded diagnostic capabilities, including the identification of microbes within tumors and their potential role in cancer progression. The aims of this study were to explore the bacterial composition in bile from patients with obstructive jaundice of different etiologies and to investigate the association between bile microbiota and biochemical analytes, as well as their potential as biomarkers for diagnosis of obstructive jaundice diseases.

METHODS: Bile samples from patients with obstructive jaundice admitted to Beijing Friendship Hospital were collected and subjected to 16S rRNA and metagenomic sequencing. The study included patients diagnosed with benign biliary stricture, gallstone, and CHOL. Clinical data and bile chemical components were analyzed. The potential functional roles of the identified microbiota were predicted using bioinformatics tools.

RESULTS: The study enrolled 13 patients with benign biliary stricture, 19 with gallstones, and 10 with CHOL. Significant differences in bile chemical components and microbial diversity were observed among the groups. The bile microbiota was dominated by distinct phyla and genera across the groups, with Proteobacteria and Fusobacteriota enriched in benign biliary stricture, Firmicutes and Desulfobacterota in CHOL, and Synergistota in patients with gallstone. Functional analysis revealed differences in gene functions related to metabolism and other biological processes. A correlation between bile microbiota and biochemical markers was established, and the combination of differential microbiota showed potential as a diagnostic marker for obstructive jaundice of different etiologies.

DISCUSSION: Bile microbiota varies significantly among patients with obstructive jaundice of different etiologies. The identified microbial signatures and their functional roles could serve as novel diagnostic markers and provide insights into the pathogenesis of biliary diseases.}, } @article {pmid40135668, year = {2025}, author = {Nassar, R and Nassar, M and Mohamed, L and Senok, A and Williams, D}, title = {Characterization and ex vivo modelling of endodontic infections from the Arabian Gulf region.}, journal = {International endodontic journal}, volume = {58}, number = {7}, pages = {1091-1108}, pmid = {40135668}, issn = {1365-2591}, support = {MBRU-CMRG2020-11//Mohammed Bin Rashid University of Medicine and Health Sciences/ ; 2201100262//University of Sharjah/ ; }, mesh = {Humans ; *Biofilms/growth & development ; *Dental Pulp Necrosis/microbiology ; Adult ; *Dental Pulp Cavity/microbiology ; Male ; Female ; Microbiota ; Metagenomics ; Middle Aged ; }, abstract = {AIM: The microbiota of endodontic infections in patients from the Arabian Gulf region (AGR) is largely unexplored. While research in different global regions has investigated the microbial composition of such infections, studies using shotgun metagenomic sequencing (SMS) alongside culture-dependent techniques (CDT) are limited. There are also few in vitro biofilm models that reflect the microbial profiles of endodontic infections. Therefore, by employing SMS and CDT, this research aimed to explore compositional and functional microbial profiles of endodontic infections from the AGR. The research also sought to develop ex vivo biofilms directly from endodontic infection samples.

METHODOLOGY: SMS and CDT were used to analyze 32 root canal samples from necrotic pulp. Patients' samples were categorized into two cohorts: symptomatic (n = 19) and asymptomatic (n = 13). Samples underwent sequencing followed by bioinformatic analysis to investigate microbial composition, resistome, virulome, and functional differences. Two representative samples (8R, 15R) were selected to develop ex vivo biofilms on hydroxyapatite coupons. Similarity between inoculum and developed biofilms was assessed using SMS and CDT. The reproducibility of developed biofilms was assessed based on microbial composition and relative abundance at the species level using correlation coefficient analysis.

RESULTS: Endodontic samples had high bacterial diversity, with a total of 366 bacterial species detected across the two cohorts. Several antibiotic resistance (n = 59) and virulence (n = 82) genes were identified, with no significant differences between the cohorts. CDT identified 28 bacterial species, with 71.4% of the isolated bacteria having phenotypic resistance to clinically relevant antibiotics. SMS showed that the ex vivo biofilms were polymicrobial. Biofilm derived from sample 15R had 9 species and was dominated by Enterococcus faecalis, while sample 8R had 12 species and was dominated by Streptococcus mutans. Pearson correlation analysis demonstrated a significant positive correlation between biological biofilm replicates, confirming the reproducibility of biofilm formation.

CONCLUSIONS: There was high bacterial diversity in root canal samples from necrotic pulp. Samples were shown to contain antibiotic resistance and virulence genes, with no differences evident between symptomatic and asymptomatic infections. A high number of isolated bacteria were resistant to clinically used antibiotics. Ex vivo biofilm models from clinical samples were successfully developed and reproducibly reflected a polymicrobial composition.}, } @article {pmid40135504, year = {2025}, author = {Pelto, J and Auranen, K and Kujala, JV and Lahti, L}, title = {Elementary methods provide more replicable results in microbial differential abundance analysis.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40135504}, issn = {1477-4054}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Reproducibility of Results ; }, abstract = {Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.}, } @article {pmid40133298, year = {2025}, author = {Bhanu, P and Buchke, S and Hemandhar-Kumar, N and Varsha, P and Kiran, SKR and Vikneswaran, G and Alva, A and Basavaraj, GS and Kumar, J}, title = {Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10303}, pmid = {40133298}, issn = {2045-2322}, support = {20210001//Bangalore Bioinnovation Centre/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Mouth/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; SARS-CoV-2 ; Male ; Female ; Adult ; Middle Aged ; Case-Control Studies ; }, abstract = {COVID-19, caused by SARS-CoV-2, affects multiple body systems, including the oral cavity, where it may disrupt the oral microbiome in ways that contribute to disease pathology. Understanding the long-term interaction between SARS-CoV-2 and the oral microbiome is crucial, as it may reveal microbial markers valuable for diagnosing or monitoring persistent health issues in COVID-19 survivors. Metagenomic sequencing revealed significant microbial shifts in the oral microbiome of COVID-19 patients, showing reduced microbial diversity and increased prevalence of opportunistic pathogens compared to healthy individuals. Alpha diversity measures indicated lower microbial diversity and evenness, while beta diversity analyses demonstrated distinct microbial community compositions. Core microbiome analysis identified unique taxa in COVID-19 patients that may contribute to disease pathology, while differential abundance analysis highlighted specific taxa shifts, including an increase in potential pathogens. Our findings advance the understanding of microbial changes in the oral microbiome associated with COVID-19 and suggest potential targets for microbiome-based interventions. While these results indicate associations with possible health impacts, further research is needed to determine causative links and long-term implications for COVID-19 survivors. This foundational research highlights the potential for microbiome science to inform diagnostic tools, such as microbial markers for disease progression, and therapeutic approaches, including targeted probiotics, which could ultimately support better patient outcomes and public health strategies.}, } @article {pmid40132505, year = {2025}, author = {Wang, L and Zhang, W and Yao, J and Qi, Z and Liu, Y and Li, Z and Qu, J and Ma, Y and Zhang, Y}, title = {Effect of freeze-thaw cycle aging on biochar application in DEHP contaminated Mollisols: Insights from soil properties and microbial community.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118082}, doi = {10.1016/j.ecoenv.2025.118082}, pmid = {40132505}, issn = {1090-2414}, mesh = {*Charcoal/chemistry ; *Soil Microbiology ; *Soil Pollutants/analysis/metabolism ; *Diethylhexyl Phthalate/metabolism/analysis ; Soil/chemistry ; Biodegradation, Environmental ; Freezing ; China ; Microbiota ; *Environmental Restoration and Remediation/methods ; }, abstract = {Biochar holds significant promise for remediation of organic pollutants. However, the impact of biochar on di-(2-ethylhexyl) phthalate (DEHP)-contaminated Mollisols after freeze-thaw cycles is largely unknown, according to the seasonal traits observed at high latitudes. In this study, fresh biochar (BC) was produced from corn straw, and freeze-thaw aging biochar (FBC) was prepared by simulating winter temperatures in the Mollisol region of Northeast China using BC as a precursor. Pot experiments were conducted to evaluate the effects of freeze-thaw aging on the detoxification efficiency of biochar, the improvement of soil physical and chemical properties, and the regulation of soil microbial community structure and functional genes. The results indicated that biochar after freeze-thaw cycling significantly improved the physical and chemical properties of Mollisols compared with the control, reducing DEHP content by 99.08 % after 28 days. Metagenomic sequencing further revealed the presence of microorganisms and genetic elements potentially involved in DEHP degradation in the soil. The treatment group with freeze-thaw aging biochar exhibited higher microbial diversity and abundance, particularly in Proteobacteria, Bacteroides, and Firmicutes. Analysis of the DEHP degradation pathway via benzoic acid route revealed an increase in the abundance of degraded functional genes/enzymes (benC-xylZ, pacL, catB, pcaG, mhpE, and mhpF). The up-regulation of nitrogen fixation genes and nitrification genes (amoB, hao, narG, nifD, and vnfH) along with a 49.19 % increase in soil microbial biomass nitrogen suggested that freeze-thaw aging biochar benefited nitrogen cycling. Furthermore, the feasibility of applying biochar to high-latitude agricultural settings was validated using pakchoi (Brassica rapa L. ssp. chinensis) as a test crop. These findings suggest that the freeze-thaw aging process enhances the effectiveness of biochar in remediating DEHP-contaminated Mollisols. This study offers a novel perspective on the restoration and improvement of Mollisol productivity in high-latitude regions through biochar application.}, } @article {pmid40132013, year = {2025}, author = {Halo, BA and Aljabri, YAS and Yaish, MW}, title = {Drought-induced microbial dynamics in cowpea rhizosphere: Exploring bacterial diversity and bioinoculant prospects.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0320197}, pmid = {40132013}, issn = {1932-6203}, mesh = {*Rhizosphere ; *Droughts ; *Vigna/microbiology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Soil Microbiology ; Phylogeny ; Plant Roots/microbiology ; Microbiota ; Metagenomics ; }, abstract = {Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.}, } @article {pmid40131463, year = {2025}, author = {Liu, H and Gan, Y and He, B and Liu, H and Zhuo, H and Tang, J and Xie, B and Shen, G and Ren, H and Jiang, X}, title = {mNGS technique was used to analyze the microbiome structure of intervertebral disc tissue in 99 patients with degenerative disc disease.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {34}, number = {5}, pages = {1709-1721}, pmid = {40131463}, issn = {1432-0932}, mesh = {Humans ; *Intervertebral Disc Degeneration/microbiology ; Male ; Female ; Middle Aged ; *Intervertebral Disc/microbiology ; *Microbiota ; Adult ; *Lumbar Vertebrae/microbiology ; Aged ; }, abstract = {OBJECTIVE: Whether bacterial hypotoxic infection in the intervertebral disc is the cause of disc degenerative disease (DDD) is controversial. The mNGS technique can provide valuable insights by obtaining more comprehensive evidence of the presence of bacteria in the intervertebral disc. This study was designed to analyze the characteristics of intervertebral microbiome structure in patients with lumbar disc degenerative disease and its correlation with clinical indicators.

METHODS: A total of 104 patients with lumbar disc degenerative diseases were included in this study. The surgically removed lumbar intervertebral disc tissues were collected for clinical culture and metagenomic second-generation sequencing (mNGS), and the consistency of the two microbial detection methods was compared.According to the collected clinical information, patients were grouped according to the modified Pfirrmann grading, Modic typing and age, and the differences of microbial communities detected by mNGS among different groups were compared, including α diversity analysis, β diversity analysis, species abundance difference analysis, etc. Spearman correlation between clinical features and generic relative abundance was calculated.

RESULTS: The effective culture results of 104 intervertebral disc tissue samples were only 19 cases positive, with a positive rate of 18.3% (19/104), and the mNGS detection results were positive in 99 cases, with a positive rate of 95.2% (99/104). According to the 19 samples with positive culture, nearly half 47.4% (9/19) of staphylococcus species were positive, and all the positive species were basically epidermal common colonization species or environmental common bacteria. At the same time, we conducted two times of mNGS sequencing for these 19 samples, and the consistency rate between the two sequencing results and the culture results was 84.2% (16/19). According to the results of mNGS detection, 250 species from 110 genera were detected in 99 positive samples. The results of group analysis showed that patients with lower degree of disc degeneration (modified Pfirrmann ≤ 4) and young patients (age < 45 years) had more abundant microbial communities in disc tissue (P < 0.05). Correlation analysis showed that there was a positive correlation between Arcobacter skirrowii and improved Pfirrmann classification at the species level (P < 0.01). There was a negative correlation between pseudomonas thermotolerans and modified Pfirrmann classification (P < 0.05). There was a positive correlation between Staphylococcus hominis and Modic typing scores (P < 0.05). Staphylococcus arlettae was negatively correlated with age (P < 0.05). At the genus level, Arcobacter had a significant positive correlation with the modified Pfirrmann grade and Modic classification (P < 0.05), Corynebacterium had a significant negative correlation with the modified Pfirrmann grade (P < 0.05), and Pseudomonas had a significant negative correlation with age (P < 0.05). After our follow-up of six months to one year, two of the patients included in this study eventually developed severe lumbar disc infection, and the rest did not develop infection.

CONCLUSIONS: This study proves that hypotoxic infection may be involved in the degeneration of intervertebral disc, and the bacterial species that cause this occult infection may be more abundant than previously thought. In addition, there was a significant correlation between the biome structure of these bacteria and clinical indicators. The hypothesis of the cause of this insidious infection has the potential to change the way the disease is treated.}, } @article {pmid40131312, year = {2025}, author = {Herazo-Álvarez, J and Mora, M and Cuadros-Orellana, S and Vilches-Ponce, K and Hernández-García, R}, title = {A review of neural networks for metagenomic binning.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, pmid = {40131312}, issn = {1477-4054}, support = {2022-21221825//National Agency for Research and Development/ ; EQM210185//Fondequip/ ; }, mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Metagenome ; Humans ; Microbiota ; Machine Learning ; Deep Learning ; }, abstract = {One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.}, } @article {pmid40129931, year = {2025}, author = {Lee, G and Rosa, BA and Fernandez-Baca, MV and Martin, J and Ore, RA and Ortiz, P and Cabada, MM and Mitreva, M}, title = {Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1555171}, pmid = {40129931}, issn = {2235-2988}, mesh = {Peru ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Triclabendazole/therapeutic use ; Animals ; *Fascioliasis/drug therapy/microbiology/parasitology ; *Fasciola hepatica/drug effects ; Male ; Female ; *Anthelmintics/therapeutic use ; Treatment Outcome ; Adult ; Metagenomics ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; }, abstract = {BACKGROUND: Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.

METHODS: In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.

RESULTS AND DISCUSSION: Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.

CONCLUSIONS: Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.}, } @article {pmid40129261, year = {2025}, author = {Boden, JS and Som, SM and Brazelton, WJ and Anderson, RE and Stüeken, EE}, title = {Evaluating Serpentinization as a Source of Phosphite to Microbial Communities in Hydrothermal Vents.}, journal = {Geobiology}, volume = {23}, number = {2}, pages = {e70016}, pmid = {40129261}, issn = {1472-4669}, support = {NE/V010824/1//Natural Environment Research Council/ ; 80NSSC19K1427//NASA Planetary Science Division ISFM Program/ ; OCE-1536405//National Science Foundation/ ; 80NSSC18K0829//NASA Astrobiology Program/ ; 80NSSC19K1427//NASA Astrobiology Program/ ; }, mesh = {*Hydrothermal Vents/microbiology/chemistry ; *Phosphites/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics ; }, abstract = {Previous studies have documented the presence of phosphite, a reduced and highly soluble form of phosphorus, in serpentinites, which has led to the hypothesis that serpentinizing hydrothermal vents could have been an important source of bioavailable phosphorus for early microbial communities in the Archean. Here, we test this hypothesis by evaluating the genomic hallmarks of phosphorus usage in microbial communities living in modern hydrothermal vents with and without influence from serpentinization. These genomic analyses are combined with results from a geochemical model that calculates phosphorus speciation during serpentinization as a function of temperature, water:rock ratio, and lithology at thermodynamic equilibrium. We find little to no genomic evidence of phosphite use in serpentinizing environments at the Voltri Massif or the Von Damm hydrothermal field at the Mid Cayman Rise, but relatively more in the Lost City hydrothermal field, Coast Range Ophiolite Microbial Observatory, The Cedars, and chimney samples from Old City hydrothermal field and Prony Bay hydrothermal field, as well as in the non-serpentinizing hydrothermal vents at Axial Seamount. Geochemical modeling shows that phosphite production is favored at ca 275°C-325°C and low water:rock ratios, which may explain previous observations of phosphite in serpentinite rocks; however, most of the initial phosphate is trapped in apatite during serpentinization, suppressing the absolute phosphite yield. As a result, phosphite from serpentinizing vents could have supported microbial growth around olivine minerals in chimney walls and suspended aggregates, but it is unlikely to have fueled substantial primary productivity in diffusely venting fluids during life's origin and evolution in the Archean unless substrates equivalent to dunites (composed of > 90 wt% olivine) were more common.}, } @article {pmid40128855, year = {2025}, author = {DeVeaux, AL and Hall-Moore, C and Shaikh, N and Wallace, M and Burnham, CD and Schnadower, D and Kuppermann, N and Mahajan, P and Ramilo, O and Tarr, PI and Dantas, G and Schwartz, DJ}, title = {Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {82}, pmid = {40128855}, issn = {2049-2618}, support = {T32GM139774/GM/NIGMS NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; R01 AI155893/AI/NIAID NIH HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Infant ; *Metagenomics/methods ; Infant, Newborn ; Feces/microbiology ; *Fever/microbiology ; Urinary Tract Infections/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Bacterial Infections/microbiology ; Case-Control Studies ; Metagenome ; Bacteremia/microbiology ; }, abstract = {BACKGROUND: Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.

RESULTS: We studied a cohort of febrile term infants < 60 days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (> 99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.

CONCLUSIONS: The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.}, } @article {pmid40128848, year = {2025}, author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC}, title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {81}, pmid = {40128848}, issn = {2049-2618}, support = {P30-ES002109//NIEHS Core Center Grant/ ; R01-OD028099-01//NIH Transformative Award/ ; R01 CA281732/CA/NCI NIH HHS/United States ; T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; T32 ES007020/ES/NIEHS NIH HHS/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; Mice ; Animals ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Epigenesis, Genetic ; *Epigenome ; *Phosphates/metabolism ; Metagenome ; Female ; Male ; Mass Spectrometry ; }, abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.

RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.}, } @article {pmid40128575, year = {2025}, author = {Yun, H and Seo, JH and Kim, YG and Yang, J}, title = {Impact of scented candle use on indoor air quality and airborne microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10181}, pmid = {40128575}, issn = {2045-2322}, support = {RS-2023-00244833//National Research Foundation of Korea/ ; }, mesh = {*Air Pollution, Indoor/analysis ; *Air Microbiology ; *Microbiota ; Particulate Matter/analysis ; Humans ; Environmental Monitoring ; Bacteria/genetics/classification/isolation & purification ; Air Pollutants/analysis ; *Odorants/analysis ; }, abstract = {Indoor air quality has become a growing concern worldwide due to its significant impact on human health, particularly in residential environments where people spend most of their time. Many studies have examined particulate matter (PM) in indoor air and indoor bioaerosols. However, there is a significant lack of research on airborne micro-sized bacteria (m-AB) and nano-sized bacterial extracellular vesicles (n-ABE), particularly those produced by common household activities, such as burning scented candles. This study investigates changes in PM concentrations and indoor microbiome composition resulting from candle use. Air samples were collected from three locations in residential homes: at the candle-lit spot (CL), 3 m away (3m_CL), and 6 m away (6m_CL). PM10 concentrations peaked at 1.52 times the baseline at the source after 5 min of burning, while PM2.5 and PM1 remained elevated at 3m_CL and 6m_CL over time. Before burning, dominant m-AB genera included Phyllobacterium and Pseudomonas, while post-burning, Phyllobacterium myrsinacearum in n-ABE significantly increased, marking its first detection in indoor air. This suggests that existing airborne bacteria may undergo growth or apoptosis due to combustion byproducts. These findings highlight the importance of improving ventilation in indoor spaces to minimize health risks from prolonged exposure to airborne particles and bacterial vesicles.}, } @article {pmid40128181, year = {2025}, author = {Yan, W and Shi, X and Zhao, Y and Liu, X and Jia, X and Gao, L and Yuan, J and Liao, A and Yasui, H and Wang, X and Wang, X and Zhang, R and Wang, H}, title = {Microbiota-reprogrammed phosphatidylcholine inactivates cytotoxic CD8 T cells through UFMylation via exosomal SerpinB9 in multiple myeloma.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2863}, pmid = {40128181}, issn = {2041-1723}, support = {2022-YGJC-61;2022-MS-219//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Female ; Animals ; Mice ; Humans ; Cell Line ; *T-Lymphocytes, Cytotoxic/immunology ; *Gastrointestinal Microbiome ; *Phosphatidylcholines/immunology/metabolism ; *Multiple Myeloma/genetics/immunology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Exosomes/immunology/metabolism ; *Serpins/genetics/immunology/metabolism ; *Membrane Proteins/genetics/immunology/metabolism ; }, abstract = {Gut microbiome influences tumorigenesis and tumor progression through regulating the tumor microenvironment (TME) and modifying blood metabolites. However, the mechanisms by which gut microbiome and blood metabolites regulate the TME in multiple myeloma (MM) remain unclear. By employing16S rRNA gene sequencing coupled with metagenomics and ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, we find that Lachnospiraceae are high and phosphatidylcholine (PC) are low in MM patients. We further show that Lachnospiraceae inhibits PC production from MM cells and enhances cytotoxic CD8 T cell function. Mechanistically, PC promotes Sb9 mRNA maturation in MM cells by LIN28A/B via lysophosphatidic acid, thus enhances exosamal Sb9 production. Exosamal Sb9 then reduces GZMB expression by suppressing tumor protein p53 (TP53) UFMylation via the competitive binding of TP53 with the ubiquitin-fold modifier conjugating enzyme 1 in CD8 T cells. We thus show that Lachnospiraceae and PC may be potential therapeutic targets for MM treatment.}, } @article {pmid40127751, year = {2025}, author = {Lim, TW and Huang, S and Burrow, MF and McGrath, C}, title = {A randomised crossover clinical trial of the efficacy of an ultrasonic cleaner combined with a denture cleanser on the microbiome on removable dentures among community-dwelling older adults.}, journal = {Journal of dentistry}, volume = {156}, number = {}, pages = {105709}, doi = {10.1016/j.jdent.2025.105709}, pmid = {40127751}, issn = {1879-176X}, mesh = {Humans ; Cross-Over Studies ; *Denture Cleansers/therapeutic use/pharmacology ; Aged ; Female ; Male ; Single-Blind Method ; *Microbiota/drug effects ; Prospective Studies ; Biofilms/drug effects ; Aged, 80 and over ; *Denture, Partial, Removable/microbiology ; Independent Living ; Ultrasonics ; Toothbrushing ; }, abstract = {OBJECTIVE: To evaluate and characterise the microbial compositional changes of removable dentures after interventions by comparing the efficacy of the test arm (a portable self-operated ultrasonic cleaner combined with an enzymatic peroxide-based denture cleanser solution) to the control arm (immersion of the denture in the same cleanser solution followed by conventional brushing).

MATERIALS AND METHODS: A prospective, single-blind, block-randomised, two-period crossover, controlled clinical trial was conducted, involving 56 community-dwelling older adults wearing removable acrylic dentures. They were block-randomized into the test/control or control/test denture cleaning sequence. Type IIB Restriction-site Associated DNA for Microbiome metagenomic sequencing was adopted to characterize the species-resolved microbial composition for denture biofilm.

RESULTS: For the intervention effect, the overall microbial richness in both arms was not significantly different based on the Chao 1 index (P = 0.343). However, Beta diversity analysis (Jaccard qualitative distance matrix) demonstrated significant differences in the microbial community structures between the Test and Control arms after interventions, confirmed by the Permanova test (R[2] = 0.01118, P = 0.034). Among the opportunistic pathogenic bacteria, Pseudomonas aeruginosa was detected as one of the top 30 species by relative abundance at the end of the clinical trial, and Enterobacter kobei was significantly enriched in the control arm, as determined by LEfSe analysis.

CONCLUSIONS: The microbial community of denture biofilm samples after both interventions were significantly 'shifted' and had limited numbers of opportunistic pathogens, suggesting the interventions equally effective in mitigating the overall number of pathogenic bacteria.

CLINICAL SIGNIFICANCE: Denture cleaning intervention using ultrasonic cleaner combined with immersion in denture cleanser solution appears to be effective in shifting the denture microbiome with reduced pathogenic bacteria among community-dwelling denture wearers.}, } @article {pmid40126388, year = {2025}, author = {Zhang, Q and Su, T and Pan, Y and Wang, X and Zhang, C and Qin, H and Li, M and Li, Q and Li, X and Guo, J and Wu, L and Qin, L and Liu, T}, title = {Malus hupehensis leaves: a functional beverage for alleviating hepatic inflammation and modulating gut microbiota in diabetic mice.}, journal = {Food & function}, volume = {16}, number = {8}, pages = {2972-2990}, doi = {10.1039/d4fo05325g}, pmid = {40126388}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Plant Leaves/chemistry ; *Plant Extracts/pharmacology/administration & dosage ; *Diabetes Mellitus, Type 2/drug therapy ; Male ; *Malus/chemistry ; Liver/drug effects/immunology/metabolism ; Mice, Inbred C57BL ; Beverages/analysis ; Functional Food ; Inflammation ; }, abstract = {Malus hupehensis leaves (MHL), consumed as a daily beverage in Chinese folk tradition and recently recognized as a new food material, are abundant in polyphenols and bioactive compounds that demonstrate hypoglycemic, lipid-lowering, and anti-inflammatory effects. However, the antidiabetic mechanisms have not been fully elucidated. This study aimed to investigate the protective mechanisms of Malus hupehensis leaves' extract (MHLE) against type 2 diabetes mellitus (T2DM). The results showed that MHLE effectively ameliorated glucose and lipid metabolic abnormalities in db/db mice, and attenuated hepatic macrophage activation. Transcriptomic analysis of the liver revealed that MHLE primarily affects genes involved in inflammatory responses and inhibited the TLR4/MAPK pathway to reduce hepatic inflammation. Metagenomic sequencing identified changes in gut microbiota composition and showed that MHLE restored the abundance of Lachnospiraceae bacterium, Oscillospiraceae bacterium, and Clostridia bacterium while reducing the abundance of Escherichia coli, thereby ameliorating gut dysbiosis. The integrated regulation of metabolism, immune response, and the microbial environment by MHLE significantly alleviated symptoms of T2DM. This study offers strong scientific evidence for the potential use of MHL as a functional food.}, } @article {pmid40124740, year = {2025}, author = {Brucato, N and Lisant, V and Kinipi, C and Kik, A and Besnard, G and Leavesley, M and Ricaut, FX}, title = {Influence of betel nut chewing on oral microbiome in Papua New Guinea.}, journal = {Evolution, medicine, and public health}, volume = {13}, number = {1}, pages = {36-44}, pmid = {40124740}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: For thousands of years, betel nut has been used as a psychoactive agent in Asian and Oceanian populations. Betel nut chewing was associated with the alteration of human oral microbiome and with diseases such as oral cancer and periodontitis, but only in populations of Asian cultural background. We studied the influence of betel nut chewing on the oral microbiome in Papua New Guinea, where half of the population uses betel nut and the prevalence of these diseases is one of the highest in the world.

METHODOLOGY: We characterized the oral microbiomes of 100 Papua New Guineans. We defined two cohorts of betel chewers (n = 50) and non-chewers (n = 50) based on a genetic approach to identify the presence of betel nut in saliva. We statistically compared the alpha and beta microbial diversities between the two cohorts. We performed linear discriminant analyses to identify bacterial species more prevalent in each cohort.

RESULTS: We found that oral microbial diversity is significantly different between betel chewers and non-chewers. The dysbiosis observed in betel chewers, led to an increase of pathogenic bacterial species including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, known to be in the aetiology of periodontal diseases.

CONCLUSIONS AND IMPLICATIONS: Our study strongly supports the alteration of human oral microbiome by betel nut use, potentially leading to periodontal diseases. It also shows the need to consider local specificities (e.g. different habits, betel nut types, and oral microbial diversities) to better characterize the impact of betel nut chewing on health.}, } @article {pmid40122890, year = {2025}, author = {Nori, SRC and Walsh, CJ and McAuliffe, FM and Moore, RL and Van Sinderen, D and Feehily, C and Cotter, PD}, title = {Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {49}, pmid = {40122890}, issn = {2055-5008}, support = {H2020-MSCA-COFUND-2019-945385//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; *Lactobacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Lactobacillus crispatus/genetics/classification/isolation & purification ; Pregnancy ; Microbiota ; Metagenome ; Ireland ; Genome, Bacterial ; Genetic Variation ; Phylogeny ; }, abstract = {The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.}, } @article {pmid40122128, year = {2025}, author = {Zhang, D and Wang, Q and Li, D and Chen, S and Chen, J and Zhu, X and Bai, F}, title = {Gut microbiome composition and metabolic activity in metabolic-associated fatty liver disease.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2482158}, pmid = {40122128}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; China ; Adult ; *Fatty Liver/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Case-Control Studies ; Metagenomics ; Aged ; Metabolome ; Metabolomics ; Metagenome ; }, abstract = {Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from the Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS. LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to increase by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis (HS), respectively. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with β-alanine, uric acid, and L-valine. Pseudoruminococcus massiliensis has a strong positive correlation with β-alanine. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC = 0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC = 0.94) in the prediction of the MAFLD HS progress. Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predict HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis and ultimately cause MAFLD.}, } @article {pmid40121033, year = {2025}, author = {Wong, MK and Boukhaled, GM and Armstrong, E and Liu, R and Heirali, AA and Yee, NR and Tsang, J and Spiliopoulou, P and Schneeberger, PHH and Wang, BX and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {3}, pages = {}, pmid = {40121033}, issn = {2051-1426}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Immunoglobulin G/immunology ; *Neoplasms/drug therapy/immunology ; Female ; Male ; Middle Aged ; }, abstract = {BACKGROUND: Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.

METHODS: Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.

RESULTS: Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3[+] CD4[+] T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14[+] and CD16[+] monocyte populations were decreased in these individuals.

CONCLUSION: These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.}, } @article {pmid40119849, year = {2025}, author = {Riva, A and Sahin, E and Volpedo, G and Catania, NT and Venara, I and Biagioli, V and Balagura, G and Amadori, E and De Caro, C and Cerulli Irelli, E and Di Bonaventura, C and Zara, F and Sezerman, OU and Russo, E and Striano, P}, title = {Medication-resistant epilepsy is associated with a unique gut microbiota signature.}, journal = {Epilepsia}, volume = {66}, number = {7}, pages = {2268-2284}, pmid = {40119849}, issn = {1528-1167}, support = {MDBR-23-004-STXBP1//Fingerprinting a multiomics biomarker profile in patients with STXBP1-RD/ ; PNRR-MUR-M4C2 PE0000006//MNESYS/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Child ; *Drug Resistant Epilepsy/microbiology/drug therapy ; Child, Preschool ; Adolescent ; Anticonvulsants/therapeutic use ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; }, abstract = {OBJECTIVE: Dysfunction of the microbiota-gut-brain axis is emerging as a new pathogenic mechanism in epilepsy, potentially impacting on medication response and disease outcome. We investigated the composition of the gut microbiota in a cohort of medication-resistant (MR) and medication-sensitive (MS) pediatric patients with epilepsy.

METHODS: Children with epilepsy of genetic and presumed genetic etiologies were evaluated clinically and subgrouped into MR and MS. Age-matched healthy controls (HCs) were also recruited. A food diary was used to evaluate nutritional habits, and the Rome IV questionnaire was used to record gastrointestinal symptoms. The microbiota composition was assessed in stool samples through 16S rRNA. α-Diversity (AD) and β-diversity (BD) were calculated, and differential abundance analysis was performed using linear multivariable models (significance: p.adj < .05).

RESULTS: Forty-one patients (MR:MS = 20:21) with a mean age of 7.2 years (±4.6 SD) and 27 age-matched HCs were recruited. No significant differences in AD were found when comparing patients and HCs. Significant positive correlation was found between AD and age (Chao1 p.adj = .0004, Shannon p.adj = .0004, Simpson p.adj = .0028). BD depicted a different bacterial profile in the epilepsy groups compared to HCs (MS vs. HC: Bray-Curtis F = 1.783, p = .001; Jaccard F = 1.24, p = .001; MR vs. HC: Bray-Curtis F = 2.24, p = .001; Jaccard F = 1.364, p = .001). At the genus level, the epilepsy groups were characterized by a significant increase in Hungatella (MS vs. HC: +4.95 log2 change; MR vs. HC: +6.72 log2 change); the [Eubacterium] siraeum group changed between the MR and MS subgroups.

SIGNIFICANCE: Epileptic patients display unique gut metagenomic signatures compared to HCs. Moreover, a different ratio of the butyrate-producing [Eubacterium] siraeum group suggests dissimilarities between patients based on the response to antiseizure medications.}, } @article {pmid40118219, year = {2025}, author = {Yan, R and Zhang, L and Chen, Y and Zheng, Y and Xu, P and Xu, Z}, title = {Therapeutic potential of gut microbiota modulation in epilepsy: A focus on short-chain fatty acids.}, journal = {Neurobiology of disease}, volume = {209}, number = {}, pages = {106880}, doi = {10.1016/j.nbd.2025.106880}, pmid = {40118219}, issn = {1095-953X}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Fatty Acids, Volatile/metabolism ; *Epilepsy/metabolism/microbiology/therapy ; Blood-Brain Barrier/metabolism ; Animals ; Dysbiosis/metabolism ; }, abstract = {According to the criteria established by the International League Against Epilepsy (ILAE), epilepsy is defined as a disorder characterized by at least two unprovoked seizures occurring more than 24 h apart. Its pathogenesis is closely related to various physiological and pathological factors. Advances in high-throughput metagenomic sequencing have increasingly highlighted the role of gut microbiota dysbiosis in epilepsy. Short-chain fatty acids (SCFAs), the major metabolites of the gut microbiota and key regulators of the gut-brain axis, support physiological homeostasis through multiple mechanisms. Recent studies have indicated that SCFAs not only regulate seizures by maintaining intestinal barrier integrity and modulating intestinal immune responses, but also affect the structure and function of the blood-brain barrier (BBB) and regulate neuroinflammation. This review, based on current literatures, explores the relationship between SCFAs and epilepsy, emphasizing how SCFAs affect epilepsy by modulating the intestinal barrier and BBB. In-depth studies on SCFAs may reveal their therapeutic potential and inform the development of gut microbiota-targeted epilepsy treatments.}, } @article {pmid40117915, year = {2025}, author = {Ghemrawi, M and Ramírez Torres, A and Netherland, M and Wang, Y and Hasan, NA and El-Fahmawi, B and Duncan, G and McCord, B}, title = {Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse.}, journal = {Forensic science international. Genetics}, volume = {78}, number = {}, pages = {103266}, doi = {10.1016/j.fsigen.2025.103266}, pmid = {40117915}, issn = {1878-0326}, mesh = {Humans ; Female ; *Metagenomics ; Male ; *Microbiota ; *Coitus ; Vagina/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Penis/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Forensic Genetics ; Proof of Concept Study ; Bacteria/genetics ; }, abstract = {The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.}, } @article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, } @article {pmid40116459, year = {2025}, author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M}, title = {Dietary protein source alters gut microbiota composition and function.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40116459}, issn = {1751-7370}, support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; 7002782//USDA National Institute of Food and Agriculture/ ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK034987/NH/NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; 7002782//USDA National Institute of Food and Agriculture, Hatch/ ; }, mesh = {Animals ; *Dietary Proteins/metabolism/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Bacteria/classification/genetics ; Mice, Inbred C57BL ; Proteomics ; Diet ; Male ; Amino Acids/metabolism ; }, abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.}, } @article {pmid40115125, year = {2025}, author = {Pavloudi, C and Santi, I and Azua, I and Baña, Z and Bastianini, M and Belser, C and Bilbao, J and Bitz-Thorsen, J and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Daguin, C and Díaz de Cerio, O and Exter, K and Fauvelot, C and Frada, MJ and Galand, PE and Garczarek, L and González Fernández, J and Guillou, L and Hablützel, PI and Heynderickx, H and Houbin, C and Kervella, AE and Krystallas, A and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhaes, C and Maidanou, M and Margiotta, F and Montresor, M and Not, F and Paredes, E and Percopo, I and Péru, E and Poulain, J and Præbel, K and Rigaut-Jalabert, F and Romac, S and Stavroulaki, M and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Trano, AC and Wincker, P and Pade, N}, title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e143585}, pmid = {40115125}, issn = {1314-2828}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.}, } @article {pmid40115072, year = {2025}, author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X}, title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1433131}, pmid = {40115072}, issn = {2235-2988}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Nervous System Diseases/microbiology/genetics ; Brain ; Genome-Wide Association Study ; Risk Factors ; }, abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.}, } @article {pmid40114290, year = {2025}, author = {Demina, T and Marttila, H and Pessi, IS and Männistö, MK and Dutilh, BE and Roux, S and Hultman, J}, title = {Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {79}, pmid = {40114290}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Virome/genetics ; *Genome, Viral ; *Metagenome ; Phylogeny ; Tundra ; *Acidobacteria/virology ; Arctic Regions ; *Bacteriophages/genetics/isolation & purification/classification ; Finland ; }, abstract = {BACKGROUND: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.

RESULTS: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.

CONCLUSIONS: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.}, } @article {pmid40114168, year = {2025}, author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S}, title = {Multiple primary malignancies and gut microbiome.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {516}, pmid = {40114168}, issn = {1471-2407}, support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Aged ; Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; *Colorectal Neoplasms/microbiology/virology ; Case-Control Studies ; Adult ; Bacteria/genetics/classification/isolation & purification ; Enterovirus/genetics/isolation & purification ; }, abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.

OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.

METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.

RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.

CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.}, } @article {pmid40111891, year = {2025}, author = {Díez-Madueño, K and Montero, I and Fernández-Gosende, M and Martínez-Álvarez, N and Hidalgo-Cantabrana, C and de la Cueva Dobao, P and Coto-Segura, P}, title = {Compositional and Functional Profile of Gut Microbiota in a Cohort of Adult Spanish Patients with Atopic Dermatitis Using Metagenomics: A Cross-Sectional Study.}, journal = {Dermatitis : contact, atopic, occupational, drug}, volume = {36}, number = {4}, pages = {358-364}, doi = {10.1089/derm.2024.0536}, pmid = {40111891}, issn = {2162-5220}, mesh = {Humans ; *Dermatitis, Atopic/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Adult ; Female ; Male ; Metagenomics ; *Dysbiosis/microbiology ; Feces/microbiology ; Middle Aged ; Spain ; Case-Control Studies ; Young Adult ; }, abstract = {Background: The role of gut dysbiosis in the pathophysiology of atopic dermatitis (AD) through immune system (IS) imbalance is a novel line of investigation currently under discussion. This study aimed to characterize compare the composition and functional profile of the gut microbiota (GM) between adults with AD and healthy individuals. Methods: Observational cross-sectional study, where fecal samples from 70 adults (38 patients and 32 controls) were analyzed using metagenomics and bioinformatics. Results: Differences between the GM of patients with AD and healthy individuals were demonstrated. Reduced microbial diversity was found in subjects with AD. Bacterial species with lower abundance primarily belonged to the families Ruminococcaceae, Akkermansiaceae, and Methanobacteriaceae. Several microbial metabolic pathways were found to be decreased in patients with AD, including amino acid biosynthesis, vitamin biosynthesis, fatty acids and lipids biosynthesis, and energy metabolism. Conclusion: Adults with AD exhibited a distinct GM compared to healthy individuals. Changes were demonstrated both compositionally and functionally. Further investigation is mandatory to elucidate the potential link and causal relationship between gut dysbiosis and AD, which may be crucial for a deeper understanding of the disease's pathophysiology and the development of novel therapeutic approaches.}, } @article {pmid40111684, year = {2025}, author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA}, title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {31-51}, pmid = {40111684}, issn = {0065-2598}, mesh = {Humans ; *Symbiosis/physiology ; *Mouth/microbiology/virology ; *Microbiota/physiology ; *Homeostasis ; *Bacteria/genetics/metabolism ; *Host Microbial Interactions/physiology ; Archaea ; Fungi ; }, abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.}, } @article {pmid40108202, year = {2025}, author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA}, title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {46}, pmid = {40108202}, issn = {2055-5008}, mesh = {Humans ; Infant ; *Prophages/genetics/isolation & purification/physiology/classification ; *Gastrointestinal Microbiome ; Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Male ; Metagenomics ; Bacteroides/virology ; }, abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.}, } @article {pmid40105325, year = {2025}, author = {Zhang, H and Lu, T and Guo, S and He, T and Shin, M-K and Luo, C and Tong, J and Zhang, Y}, title = {Rumen microbes affect the somatic cell counts of dairy cows by modulating glutathione metabolism.}, journal = {mSystems}, volume = {10}, number = {4}, pages = {e0109324}, pmid = {40105325}, issn = {2379-5077}, support = {32272904//National Natural Science Foundation of China/ ; 32373086//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; Milk/metabolism/cytology ; *Glutathione/metabolism ; Cell Count ; Cytokines/blood ; *Gastrointestinal Microbiome ; Microbiota ; Lactation ; Mastitis, Bovine/microbiology/metabolism ; Dysbiosis ; }, abstract = {Healthy mammary glands are essential for high-quality milk production in the dairy industry. The relationship between somatic cell counts (SCCs), rumen fermentation, and microbiota interactions remains unclear. This study integrated physiological indicators, high-throughput 16S rRNA gene sequencing, and metagenomics data analysis to investigate the mechanisms linking rumen microbes and mastitis and to evaluate the changes in milk production and serum cytokine levels in cows with low (L-SCC) and high (H-SCC) somatic cell counts. Compared with the L-SCC group, the H-SCC group exhibited significantly lower lactose and fat contents in milk, reduced rumen fermentation product levels, and increased abundances of Bacteroidetes, Firmicutes, Lachnospiraceae, Prevotella, and Rumiclostridium. Elevated serum levels of IgG2, IgM, IL-1β, IL-6, and TNF-ɑ in the H-SCC group indicated inflammation and rumen microbiota dysbiosis. Functional analysis of microbial communities revealed significant enrichment in pathways related to glutathione metabolism, thyroid hormone synthesis, hypertrophic cardiomyopathy (HCM), the phosphotransferase system (PTS), the P53 signaling pathway, and the Jak-STAT signaling pathway. Correlation network analysis showed that changes in bacterial families, such as Rikenellaceae, Muribaculaceae, and Prevotellaceae, were associated with cytokines, rumen fermentation, and milk quality. The study highlights the interaction between rumen microbiota homeostasis and mammary gland health, indicating that rumen fermentation status influences serum inflammation and milk quality. Modulating rumen fermentation to enhance mammary gland immune function presents a viable strategy for sustainable dairy industry development with long-lived, highly productive cows.IMPORTANCEHigh somatic cell counts (SCCs) are a key biomarker of mastitis and are associated with decreased milk production and significant economic losses in dairy farming. This study systematically examines the relationship between elevated SCCs, rumen microbial dysbiosis, and host inflammatory responses, shedding light on the intricate interplay between microbial ecosystems and host physiology. The findings highlight the potential for microbiota-targeted interventions to reduce inflammation, improve milk composition, and enhance dairy cow productivity. Rather than presuming a direct causative link between SCC-associated dysbiosis and inflammation, this research focuses on their interdependent dynamics, offering a nuanced understanding of the complex biological mechanisms involved. This work advances knowledge of host-microbiota interactions in livestock, providing practical insights for the development of innovative strategies to manage mastitis and improve overall herd health. By adhering to One Health principles, this study underscores the significance of sustainable agricultural practices that prioritize animal welfare, environmental stewardship, and food security. These findings establish a robust foundation for future research into microbiota-driven solutions aimed at enhancing the health and productivity of dairy cattle.}, } @article {pmid40102546, year = {2025}, author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T}, title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9288}, pmid = {40102546}, issn = {2045-2322}, mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; Escherichia coli/genetics/drug effects ; }, abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.}, } @article {pmid40102379, year = {2025}, author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T}, title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2683}, pmid = {40102379}, issn = {2041-1723}, support = {OPP1175213//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Female ; *Dietary Supplements ; Infant ; *Carbohydrate Metabolism/drug effects ; Pregnancy ; Adult ; Burkina Faso ; Male ; Infant, Newborn ; *Dietary Proteins/administration & dosage ; Lactation ; Feces/microbiology ; Maternal Nutritional Physiological Phenomena ; }, abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.}, } @article {pmid40101714, year = {2025}, author = {Lynn, HM and Gordon, JI}, title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.}, journal = {Cell reports methods}, volume = {5}, number = {3}, pages = {101005}, pmid = {40101714}, issn = {2667-2375}, mesh = {*Metagenome/genetics ; Animals ; Mice ; Gastrointestinal Microbiome/genetics ; Humans ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.}, } @article {pmid40101514, year = {2025}, author = {Zhang, X and Wu, L and Gu, L and Jiang, Q and He, Z and Qi, Y and Zheng, X and Xu, T}, title = {Dietary areca nut extract supplementation modulates the growth performance and immunity of Jiaji ducks (Cairina moschata).}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {104971}, pmid = {40101514}, issn = {1525-3171}, mesh = {Animals ; *Ducks/growth & development/immunology ; Dietary Supplements/analysis ; Animal Feed/analysis ; Diet/veterinary ; *Plant Extracts/administration & dosage/metabolism ; Random Allocation ; *Areca/chemistry ; Gastrointestinal Microbiome/drug effects ; Nuts/chemistry ; *Immunity, Innate/drug effects ; }, abstract = {Areca nut extract (ANE) has a variety of pharmacological effects on animals. Here, we investigated the influence of ANE on the slaughter performance and immune function of Jiaji ducks. One hundred and fifty 42-day-old healthy Jiaji ducks were randomly divided into 2 groups (5 replicates of 15 ducks each), named DCK group (control) and DNT group (treatment), respectively. Ducks in the DCK group were fed a basal diet and ducks in the DNT group were fed a basal food supplemented with 0.08 g ANE per kg of basal diet. Additionally, using proteomics, untargeted metabolomics, and metagenomics, we analyzed the impact of ANE on the protein profile of the spleen, the composition of plasma metabolites, and the structure of the cecal microbiota. The results showed that the dietary inclusion of ANE significantly increased the slaughter rate of Jiaji ducks. Proteomic analysis revealed 78 differentially expressed proteins in the spleens of ANE-treated birds, including 54 proteins up-regulated and 24 proteins down-regulated in the DNT group, mainly enriched in cell adhesion molecules and glutathione metabolic pathways. Untargeted metabolomic analysis revealed that 117 serum metabolites were differentially regulated between the ANE and DCK groups; meanwhile, KEGG pathway analysis indicated that these metabolites were mainly involved in arachidonic acid metabolism, phospholipase D signaling pathway and eicosanoids. Furthermore, a metagenomic analysis showed that the genus Methanobrevibacter was significantly downregulated in the ANE supplementation group. Combined, the results of the metagenomic and metabolomic analyses showed that the relative abundance of Prevotella was significantly lower in the ANE group than in the DCK group and that Prevotella was negatively correlated with the levels of the anti-inflammatory compound hydrocinnamic acid and the lipid metabolism regulator ganoderic acid A. This study provides a reference for the application of ANE as a supplement in the diet of Jiaji ducks.}, } @article {pmid40101486, year = {2025}, author = {Sun, J and Geng, L and Zhou, D and Teng, X and Chen, M}, title = {Gut microbiota participates in polystyrene microplastics-induced defective implantation through impairing uterine receptivity.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {124997}, doi = {10.1016/j.jenvman.2025.124997}, pmid = {40101486}, issn = {1095-8630}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; Female ; *Microplastics/toxicity ; *Polystyrenes/toxicity ; Uterus/drug effects ; }, abstract = {Microplastics (MPs) are widespread in global ecosystems and could pose risks to human health. However, crucial information on the impact of MP exposure on female reproductive health remains insufficient. In this study, we constructed an MP-exposure mice model through oral administration of polystyrene microplastics (PS-MPs) and found that it resulted in impaired uterine receptivity and defective implantation. An accumulation of plastic particles was detected in MP mice intestines. Metagenomic sequencing of feces samples indicated a structural and functional alteration of gut microbiota. Alistipes played a prominent role in MP biodegradation, while among the biodegradable functional genes, ACSL made the greatest contribution. Both had a significant increase in MP group, suggesting a potential occurrence of ferroptosis. Ferroptosis, a form of programmed cell death, is closely associated with uterine receptivity impairment and defective implantation. We detected MDA contents and ferroptosis-related proteins, and the results indicated the activation of ferroptosis in the process. Our research is the first to elucidate that exposure to MPs impairs uterine receptivity and results in deficient implantation, while also providing initial evidence that gut microbiota plays a critical role in this process.}, } @article {pmid40100697, year = {2025}, author = {Sun, J and Hirai, M and Takaki, Y and Evans, PN and Nunoura, T and Rinke, C}, title = {Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, pmid = {40100697}, issn = {2057-5858}, mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; *Archaea/genetics/classification/metabolism ; Pacific Ocean ; *Bacteria/genetics/classification/metabolism ; *Metagenome ; Phylogeny ; Microbiota/genetics ; }, abstract = {Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.}, } @article {pmid40098591, year = {2025}, author = {Hernández-Trujillo, PN and Lopez-Barón, CA and Arévalo-Pinzón, G and Trujillo-Güiza, ML and González-Duque, MI and Flórez, AM and Franco, DC and Vanegas, J}, title = {Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach.}, journal = {HIV medicine}, volume = {26}, number = {5}, pages = {785-799}, doi = {10.1111/hiv.70014}, pmid = {40098591}, issn = {1468-1293}, support = {2022218//Universidad Antonio Nariño/ ; }, mesh = {Humans ; Male ; Adult ; *Homosexuality, Male ; Metagenomics ; *HIV Infections/microbiology ; *Anal Canal/microbiology ; Middle Aged ; *Rectum/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; }, abstract = {INTRODUCTION: The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.

MATERIALS AND METHODS: In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.

RESULTS: Initially, 90 samples were collected, with 20 discarded due to having less than 200 ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p = 0.45) and beta diversity (PERMANOVA R = -0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.

CONCLUSION: Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.}, } @article {pmid40098558, year = {2025}, author = {Di Rienzi, SC and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA}, title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {6}, pages = {e70408}, pmid = {40098558}, issn = {1530-6860}, support = {//BioGaia/ ; F32 AI136404/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; //Weston Family Foundation (WFF)/ ; }, mesh = {Humans ; *Enteroendocrine Cells/immunology/metabolism ; Gene Expression Regulation ; *Hormones/genetics/metabolism ; *Limosilactobacillus reuteri/genetics/metabolism ; Stress, Physiological ; Transcription, Genetic ; Intestines/microbiology ; Microbiota ; }, abstract = {Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.}, } @article {pmid40098172, year = {2025}, author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L}, title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {343}, pmid = {40098172}, issn = {1479-5876}, mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/genetics/immunology/drug therapy ; *Gastrointestinal Microbiome/genetics ; *Computational Biology/methods ; *Lung Neoplasms/therapy/microbiology/genetics/immunology/drug therapy ; *Immunotherapy ; Treatment Outcome ; Male ; Machine Learning ; Female ; }, abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.

METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.

RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy > 90% and AUC ROC > 95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.

CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.}, } @article {pmid40097931, year = {2025}, author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D}, title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {150}, pmid = {40097931}, issn = {1471-2180}, mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Whole Genome Sequencing ; *Drug Resistance, Multiple, Bacterial/genetics ; Male ; Longitudinal Studies ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Gastrointestinal Microbiome/genetics ; Aged ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.}, } @article {pmid40097230, year = {2025}, author = {Nair, SS and Kutty Narayanan, A and Nair, K and Mallick, S and Zackariah, NM and Biswas, L and Praseedom, R and G Nair, BK and Surendran, S}, title = {Microbiota-directed intervention in living donor liver transplant recipients: protocol for a randomised double-blind placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092984}, pmid = {40097230}, issn = {2044-6055}, mesh = {Humans ; *Liver Transplantation/adverse effects/methods ; Double-Blind Method ; *Living Donors ; *Synbiotics/administration & dosage ; Randomized Controlled Trials as Topic ; Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome ; *Acute-On-Chronic Liver Failure/surgery/microbiology/therapy ; Male ; Female ; Adult ; *Postoperative Complications/prevention & control ; }, abstract = {INTRODUCTION: Acute-on-chronic liver failure (ACLF) patients have the highest propensity for post-liver transplantation (LT) infections and mortality. Liver-associated diseases have been one of the primary targets for synbiotic therapy to augment immunity and mitigate infections. However, despite multiple studies showing benefits of synbiotics in liver diseases, data on their use following LT are sparse.

METHODS AND ANALYSIS: This randomised placebo-controlled study aims to assess the impact of synbiotics in ACLF patients undergoing living donor liver transplantation (LDLT). Following randomisation by computer-generated block number sequence, 3 days prior to LDLT, the intervention arm will receive standard medical treatment and synbiotics (VSL#3 a probiotic, and Yogut, prebiotic and probiotic combination) for 6 weeks, while the control arm will receive standard medical treatment with a placebo. The patients will be followed up for 6 months to study the clinical and biochemical outcomes. The primary objective is to compare the difference in the occurrence of infectious complications between the patients who receive synbiotics versus placebo during the 6-month period following LDLT. The secondary objectives include assessing the qualitative and quantitative change in microbiota with synbiotics and LDLT, adverse reactions due to synbiotics, and post-LT morbidity and mortality. The minimum sample size comes to 71 in each group. The first 50 patients in the study protocol will undergo gut microbiome analysis using 16s metagenomic and nanopore sequencing to analyse the microbial composition before starting synbiotics/placebo and at 6 weeks after LDLT.

ETHICS AND DISSEMINATION: The study is approved by the Research Ethics Committee of Amrita Institute of Medical Sciences, Kochi, India (IEC-AIMS-2022-GISUR-203) and registered in the Clinical Trial Registry of India (CTRI) CTRI/2022/10/046327. The results of the trial will be disseminated by presentation at national/international conferences and publication in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: CTRI/2022/10/046327 - Clinical Trial Registry of India.}, } @article {pmid40096540, year = {2025}, author = {Zhang, Q and Li, J and Tuo, J and Liu, S and Liu, Y and Liu, P and Ye, L and Zhang, XX}, title = {Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40096540}, issn = {1751-7370}, support = {BE2022837//Jiangsu Province Key Research and Development Program/ ; 52200057//National Natural Science Foundation of China/ ; }, mesh = {*Sewage/microbiology ; *Bacteria/virology/genetics/classification ; *Bacteriophages/genetics ; Metagenomics ; *Metagenome ; *Microbiota ; }, abstract = {Bacteria have evolved various antiviral defense systems (DSs) to protect themselves, but how DSs respond to the variation of bacteriophages in complex bacterial communities and whether DSs function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge (AS) samples from two full-scale wastewater treatment plants over 6 years and found that DSs were widespread in AS, with 91.1% of metagenome-assembled genomes (MAGs) having more than one complete DS. The stability of the bacterial community was maintained under the fluctuations of the phage community, and DS abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of DSs to phage fluctuations. The rapid turnover of clustered regularly interspaced short palindromic repeat spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical MAGs showing significant differences in DS composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities and reveals the key roles of DSs in stabilizing bacterial community structure and function.}, } @article {pmid40094563, year = {2025}, author = {Cheng, W and Yi, L and Xu, T and Xie, Y and Zhu, J and Guan, X and Li, Q and Huang, Y and Zhao, Y and Zhao, S}, title = {The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2471785}, doi = {10.1080/10495398.2025.2471785}, pmid = {40094563}, issn = {1532-2378}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Panax notoginseng/chemistry ; Swine/microbiology ; *Plant Leaves/chemistry ; *Plant Stems/chemistry ; *Drug Resistance, Microbial/genetics ; Animal Feed/analysis ; Anti-Bacterial Agents/pharmacology ; }, abstract = {In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.}, } @article {pmid40094201, year = {2025}, author = {Masaadeh, AH and Eletrebi, M and Parajuli, B and De Jager, N and Bosch, DE}, title = {Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2479774}, pmid = {40094201}, issn = {1949-0984}, support = {K08 AI159619/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Dysbiosis/microbiology/complications ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Colitis-Associated Neoplasms/microbiology/pathology ; Disease Progression ; *Bacteria/classification/genetics/isolation & purification ; *Colorectal Neoplasms/microbiology/pathology ; Aged ; Adult ; Inflammatory Bowel Diseases/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Colitis/microbiology/complications ; Metagenomics ; }, abstract = {Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.}, } @article {pmid40091534, year = {2025}, author = {Lu, YM and Lu, JQ and Zhao, Q and Chen, J and Xiong, JB}, title = {Pathogenic mechanisms of Enterocytozoon hepatopenaei through the parasite-gut microbiome-shrimp (Litopenaeus vannamei) physiology axis.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {401-413}, pmid = {40091534}, issn = {2095-8137}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Penaeidae/microbiology/physiology/parasitology ; *Enterocytozoon/physiology/pathogenicity ; }, abstract = {The progressive impact of Enterocytozoon hepatopenaei (EHP) infection on gut microbial function in Litopenaeus vannamei remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.}, } @article {pmid40091083, year = {2025}, author = {Honda, H and Suzuki, T and Kitajima, M and Kondo, NI and Miyata, K and Utsumi, S and Yamada, M}, title = {The new era shaped by environmental genome monitoring - symposium of the japanese environmental mutagen and genome society (JEMS), 2024.}, journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society}, volume = {47}, number = {1}, pages = {6}, pmid = {40091083}, issn = {1880-7046}, abstract = {The symposium "The New Era Shaped by Environmental Genome Monitoring," held in December 2024 by the Japanese Environmental Mutagen and Genome Society (JEMS), aimed to explore the interdisciplinary collaborations that are essential for the development of new scopes in environmental genome monitoring. This event highlighted the necessity of integrating mutagenicity research with ecological assessments to enhance public health and biodiversity conservation. Presentations focused on the evolving landscape of environmental genomics, including metagenomic analyses for antibiotic resistance, viral genomic surveillance in wastewater, and innovations in noninvasive biodiversity and stress monitoring through environmental DNA and RNA. This report summarizes the key discussions and presentations from the symposium, underscoring the critical role of environmental genome monitoring in shaping future safety research.}, } @article {pmid40090954, year = {2025}, author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E}, title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2595}, pmid = {40090954}, issn = {2041-1723}, support = {2018-02835//Vetenskapsrådet (Swedish Research Council)/ ; 2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2019-03482//Vetenskapsrådet (Swedish Research Council)/ ; 2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; Phylogeny ; Humans ; *Bacteria/genetics/drug effects/classification ; Wastewater/microbiology ; Animals ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Genome, Bacterial ; *Genes, Bacterial ; }, abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.}, } @article {pmid40090144, year = {2025}, author = {Deng, B and Ren, Z and Li, Q and Zhang, Z and Xu, C and Wang, P and Zhao, H and Yuan, Q}, title = {Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system.}, journal = {Water research}, volume = {280}, number = {}, pages = {123483}, doi = {10.1016/j.watres.2025.123483}, pmid = {40090144}, issn = {1879-2448}, mesh = {Animals ; Larva/metabolism ; *Zinc/metabolism ; *Chromium/metabolism ; *Citric Acid Cycle ; *Simuliidae/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.}, } @article {pmid40087549, year = {2025}, author = {Wang, X and Shang, Y and Xing, Y and Chen, Y and Wu, X and Zhang, H}, title = {Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {142}, pmid = {40087549}, issn = {1471-2180}, support = {2022KJ177//the Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 32001228//the National Natural Science Foundation of China/ ; 32270444//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Wolves/microbiology ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; *Virulence Factors/genetics/metabolism ; Dogs/microbiology ; Animals, Zoo/microbiology ; Foxes/microbiology ; Metagenomics ; Feces/microbiology ; Animals, Wild/microbiology ; Carbohydrate Metabolism ; }, abstract = {Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.}, } @article {pmid40087044, year = {2025}, author = {Chen, B and Li, Y and Li, Z and Hu, X and Zhen, H and Chen, H and Nie, C and Hou, Y and Zhu, S and Xiao, L and Li, T}, title = {Vitamin E ameliorates blood cholesterol level and alters gut microbiota composition: A randomized controlled trial.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {35}, number = {8}, pages = {103964}, doi = {10.1016/j.numecd.2025.103964}, pmid = {40087044}, issn = {1590-3729}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; *Anticholesteremic Agents/adverse effects/therapeutic use ; *Antioxidants/adverse effects/administration & dosage/therapeutic use ; *Bacteria/metabolism/drug effects/growth & development ; Bile Acids and Salts/metabolism ; Biomarkers/blood ; *Cholesterol, LDL/blood ; *Dietary Supplements/adverse effects ; Double-Blind Method ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Grape Seed Extract/adverse effects ; Healthy Volunteers ; Time Factors ; Treatment Outcome ; *Vitamin E/adverse effects/therapeutic use ; }, abstract = {BACKGROUND AND AIMS: Antioxidants, including vitamin E (VE) and grape seed extract (GSE), as anti-aging supplementation have been widely used to improve human health. The gut microbiota plays a crucial role in health and affects the treatment effect of various interventions. However, the role of gut microbiota in VE remains unclear. This study aimed to assess the longitudinal impact of VE treatment on body health and the gut microbiota.

METHODS AND RESULTS: A randomized controlled trial was conducted with 90 healthy individuals. The participants were randomly assigned to three groups: a treatment group receiving VE, another antioxidant treatment group receiving GSE, and a control group receiving a placebo. We found that VE ameliorated blood cholesterol levels by reducing the levels of low-density lipoprotein cholesterol (LDL-C) in healthy volunteers. After the intervention, there was an increase in the relative abundance of short-chain fatty acid (SCFA)-producing bacteria and bile acid metabolizers. Specifically, the abundances of Lachnospira sp. and Faecalibacterium spp. increased in the VE. Interestingly, the gut microbiota of poor responders harbored a greater proportion of disease-associated bacterial species.

CONCLUSIONS: VE could promote health by lowering LDL-C, partly and indirectly by affecting gut bacteria with the ability to produce SCFAs or metabolize bile acids.

The clinical trial was registered on August 28, 2021. Registration number was ChiCTR2100050567 (https://www.chictr.org.cn).}, } @article {pmid40086988, year = {2025}, author = {Peng, Q and Quan, L and Zheng, H and Li, J and Xie, G}, title = {Analyzing the contribution of top-down and bottom-up methods to the construction of synthetic microbial communities in Jiuyao.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104759}, doi = {10.1016/j.fm.2025.104759}, pmid = {40086988}, issn = {1095-9998}, mesh = {Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; *Microbiota ; *Fungi/classification/genetics/metabolism/isolation & purification ; }, abstract = {The construction of synthetic microbial communities is a crucial strategy for improving the stability of microbial populations and the quality of fermented foods. Jiuyao, an essential saccharification and fermentation starter in Huangjiu production, was the focus of this study. Using metagenomics combined with culture-dependent methods, we identified 11 microbial species involved in Huangjiu fermentation. Through metagenomic analysis and simulated fermentation, Rhizopus delemar, Rhizopus microspores, Rhizopus stolonife, Rhizopus azygosporus, Saccharomycopsis fibuligera, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Pediococcus pentosaceus were determined to be the core microbial species driving the Jiuyao fermentation process. A synthetic microbial community was constructed based on these species, successfully reproducing the flavor and sensory qualities of Huangjiu while enhancing fermentation efficiency. This study provides valuable insights into the functional roles of Jiuyao-associated microbes and offers a framework for improving microbial community stability and fermentation quality in Huangjiu production.}, } @article {pmid40086981, year = {2025}, author = {Kothe, CI and Renault, P}, title = {Metagenomic driven isolation of poorly culturable species in food.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104722}, doi = {10.1016/j.fm.2025.104722}, pmid = {40086981}, issn = {1095-9998}, mesh = {*Metagenomics/methods ; *Cheese/microbiology ; *Bacteria/isolation & purification/genetics/classification/growth & development ; *Food Microbiology ; Microbiota ; Metagenome ; Phylogeny ; }, abstract = {Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.}, } @article {pmid40086705, year = {2025}, author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X}, title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.}, journal = {Gene}, volume = {952}, number = {}, pages = {149414}, doi = {10.1016/j.gene.2025.149414}, pmid = {40086705}, issn = {1879-0038}, mesh = {Humans ; *Probiotics/administration & dosage ; Female ; *Gastrointestinal Microbiome/genetics/drug effects ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Infant, Newborn ; Adult ; Feces/microbiology ; Infant ; Male ; }, abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.}, } @article {pmid40086585, year = {2025}, author = {Rawat, N and Sivanesan, S and Kanade, GS and Bafana, A}, title = {Interaction of environmental fluoride exposure and gut microbes: Potential implication in the development of fluorosis in human subjects.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {200}, number = {}, pages = {115388}, doi = {10.1016/j.fct.2025.115388}, pmid = {40086585}, issn = {1873-6351}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Fluorides/toxicity ; Male ; Female ; *Fluorosis, Dental/microbiology/etiology ; *Environmental Exposure/adverse effects ; Adult ; Middle Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; }, abstract = {Fluoride exposure primarily occurs through contaminated water and leads to fluorosis, which is a global health concern. After ingestion, fluoride is absorbed via gastrointestinal tract, where it interacts with the gut microbiota. While animal studies have explored fluoride's effects on gut microbiota, no human studies have yet been conducted. Most research emphasizes metagenomic diversity, neglecting isolation and characterization of pure cultures for further applications. Additionally, the association between gut microbiota with fluorosis outcomes in fluoride-exposed populations is unexplored. This study characterizes and compares the cultivable gut microbiota in the fluoride-exposed population with (symptomatic, group II) or without (asymptomatic, group I) signs of skeletal fluorosis along with unexposed control (group III). Group I displayed higher abundance of Firmicutes (58.58 %), group II had predominance of Proteobacteria (61.25 %) while group III showed similar abundance of Proteobacteria (50.38 %) and Firmicutes (49.51 %). On analyzing short-chain fatty acid (SCFA) profiles, group I isolates produced higher isobutyric acid (1.31 ± 0.9 mM) than group II (0.71 ± 0.35 mM), while group II produced more isovaleric acid (0.8 ± 0.41 mM) than group I (0.61 ± 0.08 mM) (p < 0.05). These findings suggest that gut microbiota and SCFAs alteration may influence bone metabolism, affecting the fluorosis progression.}, } @article {pmid40086306, year = {2025}, author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D}, title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179109}, doi = {10.1016/j.scitotenv.2025.179109}, pmid = {40086306}, issn = {1879-1026}, mesh = {Animals ; *Amphipoda/microbiology ; *Gastrointestinal Microbiome ; *Plastics/metabolism ; *Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; }, abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.}, } @article {pmid40086246, year = {2025}, author = {Han, NN and Yang, JH and Wu, GG and Yang, JH and Jin, JA and Fan, NS and Jin, RC}, title = {Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137886}, doi = {10.1016/j.jhazmat.2025.137886}, pmid = {40086246}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine/pharmacology ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Oxidation-Reduction ; *Ammonia/metabolism ; Anaerobiosis ; Pseudomonas/genetics/drug effects/metabolism ; *Microbial Consortia ; }, abstract = {Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.}, } @article {pmid40084893, year = {2025}, author = {Yuan, S and Wu, Y and Balcazar, JL and Wang, D and Zhu, D and Ye, M and Sun, M and Hu, F}, title = {Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0029625}, pmid = {40084893}, issn = {1098-5336}, support = {42277115, 42177113, 42277418//National Natural Science Foundation of China/ ; Modern Agriculture BE2022322//Key P&D Project of Jiangshu Province/ ; 2024M761435//China Postdoctoral Science Foundation/ ; }, mesh = {*Bacteriophages/genetics/metabolism ; *Soil Microbiology ; Composting ; Manure/microbiology ; *Carbon Sequestration ; *Soil/chemistry ; Swine ; *Bacteria/metabolism/genetics/virology ; Animals ; *Microbiota ; Carbon/metabolism ; }, abstract = {The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.}, } @article {pmid40083550, year = {2025}, author = {Ng, HY and Liao, Y and Cheung, CL and Zhang, R and Chan, KH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1534787}, pmid = {40083550}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/immunology ; Adult ; *BNT162 Vaccine/immunology ; Antibodies, Viral/blood/immunology ; *Immunogenicity, Vaccine ; *COVID-19/immunology/prevention & control ; Antibodies, Neutralizing/blood/immunology ; Prospective Studies ; *COVID-19 Vaccines/immunology ; Hong Kong ; }, abstract = {INTRODUCTION: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity.

METHODS: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day 180 after first dose, and tested for neutralizing antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day 180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites.

RESULTS: Of 242 subjects (median age: 50.2 years [IQR:42.5-55.6]; male:85 [35.1%]), 61 (25.2%) were high-responders while 33 (13.6%) were extreme-high responders (defined as NAb≥200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans-aOR: 1.87, 95% CI: 1.02-3.51; P. excrementihominis-aOR: 2.2, 95% CI: 1.18-4.18; S. salivarius-aOR: 2.09, 95% CI: 1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00, 95% CI:1.81-107.2) and isoleucine (aOR:1.17, 95% CI:1.04-1.35) significantly associated with extreme-high vaccine response.

CONCLUSION: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.}, } @article {pmid40082612, year = {2025}, author = {Đokić, J and Dinić, M and Soković Bajić, S and Bisenić, A and Mitrović, H and Jakovljević, S and Radojević, D and Brdarić, E and Lukić, J and Živković, M and Tolinački, M and Terzić-Vidojević, A and Golić, N}, title = {High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8741}, pmid = {40082612}, issn = {2045-2322}, support = {Grant IDEAS No. 7744507, NextGenBiotics//Science Fund of the Republic of Serbia/ ; Grant No. 451-03-66/2024-03/200042//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Brain/metabolism ; Workflow ; *Anti-Inflammatory Agents/metabolism ; Probiotics ; *Bacteria/genetics/metabolism/growth & development ; }, abstract = {The gut microbiota is deeply interconnected with the brain, a phenomenon often referred to as the gut-brain axis. Dysfunction in the microbiota-gut-brain axis can cause various neurological and psychiatric disorders associated with chronic inflammation and gut microbiota dysbiosis. Therefore, cultivation of anaerobic human gut microbiota strains, and characterization of their safety status and immunomodulatory potential could contribute to deciphering the molecular mechanisms underlying the microbiota-gut-brain communication and revealed their biotherapeutic potential. However, poor cultivability of gut microbiota members, makes research into their physiological role challenging. Hence, we report a high-throughput workflow based on targeted cultivation linked to metagenome sequencing, combined with the bioinformatic search for gut members with anti-inflammatory properties which produce the most important microbial metabolites that affect brain function. With this approach, we isolated 147 bacterial strains, and 41 were characterized for their immunomodulatory status with 12 strains showing immunosuppressive features with ability of producing brain important metabolites. Through this workflow we established the best growing conditions essential for cultivation, archiving, phenotyping, and characterization of anaerobic gut bacteria important for microbiota-gut-brain-axis research, and characterized the safety and probiotic potential of 7 extremely oxygen-sensitive strains.}, } @article {pmid40082024, year = {2025}, author = {Yin, F and Ge, T and Zalucki, MP and Xiao, Y and Peng, Z and Li, Z}, title = {Gut symbionts affect Plutella xylostella (L.) susceptibility to chlorantraniliprole.}, journal = {Pesticide biochemistry and physiology}, volume = {209}, number = {}, pages = {106327}, doi = {10.1016/j.pestbp.2025.106327}, pmid = {40082024}, issn = {1095-9939}, mesh = {Animals ; *ortho-Aminobenzoates/pharmacology ; *Insecticides/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; Insecticide Resistance/genetics ; *Moths/microbiology/drug effects ; Larva/drug effects/microbiology ; }, abstract = {Plutella xylostella, a globally economically important pest of cruciferous crops, has varying degrees of resistance to almost all insecticides. Insect gut microbiotas have a variety of physiological functions, and recent studies have shown that they have some potential connection with insecticide resistance. Here, we use metagenomics to analyze the differences in gut microbiota among 5 different populations of P. xylostella resistant to chlorantraniliprole. Differential gene expression was enriched in various metabolic pathways including carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, nucleotide metabolism and so on. Proteobacteria was the dominate phyla, and the relative abundance of common dominant genera in the treated group (CL, Bt, and BtCL) was higher than that in susceptible controls. We successfully isolated 15 species of bacteria, in which the Enterobacter hormaechei was associated with enhanced insecticide resistance. The population we isolated can metabolize chlorantraniliprole in vitro, with a metabolic rate of 34.8 % within 4 days. Our work advances understanding of the evolution of insecticide resistance and lays a foundation for the further exploration of symbiotic microbial associations of lepidopteran insects and their ecological consequences.}, } @article {pmid40082000, year = {2025}, author = {Massaro, CA and Meade, S and Lemarié, FL and Kaur, G and Bressler, B and Rosenfeld, G and Leung, Y and Williams, AJ and Lunken, G}, title = {Gut microbiome predictors of advanced therapy response in Crohn's disease: protocol for the OPTIMIST prospective, longitudinal, observational pilot study in Canada.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e094280}, pmid = {40082000}, issn = {2044-6055}, mesh = {Female ; Humans ; Male ; British Columbia ; Canada ; *Crohn Disease/microbiology/therapy/drug therapy ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Longitudinal Studies ; Pilot Projects ; Prospective Studies ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis, is characterised by chronic and relapsing inflammation of the gastrointestinal tract, leading to significant morbidity and reduced quality of life. The global rise in IBD incidence is driven by a complex interplay of genetic, environmental, dietary and microbiome-related factors. Despite advancements in treatment, such as biologics, response rates remain variable, highlighting the need for personalised approaches. Recent research suggests that specific microbiome signatures may serve as biomarkers for predicting therapeutic efficacy, offering a potential tool for optimising treatment strategies in CD. The aim of the Optimising IBD Patient Treatment with Integrated Microbiome Investigation for Specialised Therapeutics (OPTIMIST) study is to evaluate microbiome profiles across various sample types in a Canadian CD cohort starting or already on advanced therapy, with the goal of developing predictive models for personalised therapeutics.

METHODS AND ANALYSIS: This study is a two-phase, longitudinal, prospective observational pilot study conducted in British Columbia, Canada, involving both CD patients and non-IBD controls. Phase 1 focuses on baseline microbiome differences across participant cohorts through cross-sectional analysis. Phase 2 follows participants over 12 months to assess microbiome changes and their association with treatment response. Stool samples, intestinal biopsies from the left colon, right colon and ileum, as well as mucosal wash samples from the proximal part of the distal colon, will undergo metagenomics, metaproteomics and metabolomics analyses to explore compositional and functional differences. Data will be analysed using alpha and beta diversity metrics, differential abundance analyses and multivariate analyses to identify microbiome-based predictors of therapeutic response.

ETHICS AND DISSEMINATION: Ethical approval was received by the Research Ethics Board (REB) of University of British Columbia-Providence Healthcare (UBC-PHC) with a REB number H23-02927. All amendments to the protocol are reported and adapted based on the requirements of the REB. The results of this study will be submitted to peer-reviewed journals and will be communicated in editorials/articles by the IBD Centre of BC and BC Children's Hospital Research Institute.

TRIAL REGISTRATION NUMBER: NCT06453720.

PROTOCOL VERSION: 2024-06-21, version 3.0.}, } @article {pmid40081757, year = {2025}, author = {Armengaud, J}, title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.}, journal = {Journal of proteomics}, volume = {316}, number = {}, pages = {105430}, doi = {10.1016/j.jprot.2025.105430}, pmid = {40081757}, issn = {1876-7737}, mesh = {Humans ; *Proteomics/methods ; *Microbiota/physiology ; Metabolomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.}, } @article {pmid40081368, year = {2025}, author = {Dai, R and Zhang, J and Liu, F and Xu, H and Qian, JM and Cheskis, S and Liu, W and Wang, B and Zhu, H and Pronk, LJU and Medema, MH and de Jonge, R and Pieterse, CMJ and Levy, A and Schlaeppi, K and Bai, Y}, title = {Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns.}, journal = {Cell}, volume = {188}, number = {9}, pages = {2521-2539.e22}, doi = {10.1016/j.cell.2025.02.013}, pmid = {40081368}, issn = {1097-4172}, mesh = {*Plant Roots/microbiology/virology ; *Genome, Viral/genetics ; *Microbiota/genetics ; *Crops, Agricultural/microbiology/virology ; *Bacteria/genetics/classification ; Phylogeny ; *Genome, Bacterial/genetics ; Soil Microbiology ; Metagenomics ; Zea mays/microbiology/virology ; Oryza/microbiology/virology ; Metagenome ; Triticum/microbiology/virology ; }, abstract = {Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.}, } @article {pmid40079420, year = {2025}, author = {Jurburg, SD}, title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14102}, pmid = {40079420}, issn = {1755-0998}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.}, } @article {pmid40077957, year = {2025}, author = {Ma, Z and Wen, X and Zhang, Y and Ai, Z and Zhao, X and Dong, N and Dou, X and Shan, A}, title = {Thymol Alleviates Colitis by Modulating Intestinal Barrier Damage, Gut Microbiota, and Amino Acid Metabolic Pathways.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {12}, pages = {7211-7227}, doi = {10.1021/acs.jafc.4c10406}, pmid = {40077957}, issn = {1520-5118}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/microbiology/drug therapy/metabolism/genetics ; *Thymol/administration & dosage ; *Amino Acids/metabolism ; Male ; Mice, Inbred C57BL ; *Intestinal Mucosa/metabolism/drug effects/microbiology ; Humans ; Bacteria/genetics/classification/isolation & purification/metabolism/drug effects ; Metabolic Networks and Pathways/drug effects ; Colon/metabolism/drug effects/microbiology ; Dextran Sulfate/adverse effects ; Cytokines/genetics/metabolism ; }, abstract = {Thymol (THY) is a phenolic monoterpene compound that has garnered attention due to its various biological properties, including antioxidant, anti-inflammatory, and immune-regulatory effects. The purpose of this study was to determine the therapeutic and protective effects of THY in colitic mice, with a particular focus on the mechanisms involving gut microbiota. The results showed that early intervention with THY (40 and 80 mg/kg) not only alleviated the clinical symptoms and colonic damage in mice with dextran sodium sulfate (DSS)-induced colitis but also suppressed the colonic production of inflammatory cytokines (IL-1β, IL-6, and IL-18) and enhanced the expression of mucins (MUC1 and MUC2) and trefoil factor family 3 (TFF3), thereby improving the integrity of the intestinal epithelial barrier. In addition, THY altered the composition of the gut microbiota in colitis mice by increasing the abundance of Bacteroides and reducing the abundance of Proteobacteria. Fecal microbial transplantation (FMT) results demonstrated that FM from THY donor mice significantly improved symptoms of inflammatory bowel disease (IBD), confirming the crucial role of the gut microbiota. Metagenomic and untargeted metabolomic studies found that the characteristic microbiota of THY is Prevotellaceae, and THY significantly upregulated the amino acid metabolic pathways related to arginine and proline metabolism, arginine biosynthesis, and glycerophospholipid metabolism. In summary, THY holds significant potential as a functional additive to enhance host intestinal activity.}, } @article {pmid40077671, year = {2025}, author = {Gao, Y and Borjihan, Q and Zhang, W and Li, L and Wang, D and Bai, L and Zhu, S and Chen, Y}, title = {Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, pmid = {40077671}, issn = {2072-6643}, support = {2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; }, mesh = {Animals ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Fecal Microbiota Transplantation/adverse effects ; *Irritable Bowel Syndrome/therapy/microbiology/etiology/metabolism ; Mice ; Disease Models, Animal ; Feces/microbiology/chemistry ; Male ; Mice, Inbred C57BL ; Serotonin/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Tryptophan/metabolism ; Metabolomics ; Dysbiosis ; Metagenomics ; }, abstract = {Background/Objectives: Irritable bowel syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Emerging evidence implicates gut microbiota dysbiosis in IBS pathogenesis, and probiotic interventions targeting microbial modulation hold therapeutic promise. Methods: this study used fecal microbiota transplantation to establish a mouse model of IBS before evaluating the effects of the complex probiotic by using metagenomics and targeted metabolomics to explore the potential mechanism. Results: After 14 days, the probiotic relieved constipation, reduced inflammation and intestinal permeability, lowered 5-HT levels and increased serotonin transporter (SERT) expression in tissues. Metagenomic analysis showed a reduced inflammation-related species abundance. It also decreased fecal butyric acid, acetic acid and tryptophan levels in IBS mice. Conclusions: The probiotic complex effectively alleviated IBS symptoms in mice by modulating gut microbiota and fecal metabolites, providing insights for future IBS research and treatment.}, } @article {pmid40076957, year = {2025}, author = {Kumagai, K and Ishikawa, S and Iino, M and Edamatsu, K and Okuyama, N and Yusa, K and Shimizu, Y and Aoki, R and Masuda, C and Ohashi, Y and Horie, A and Hoshi, K and Hamada, Y}, title = {Characterization of Salivary Microbiota in Japanese Patients with Oral Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, pmid = {40076957}, issn = {1422-0067}, support = {JP 22K10113//JSPS KAKENHI Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Humans ; *Mouth Neoplasms/microbiology ; *Saliva/microbiology ; Female ; *Microbiota/genetics ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; Japan ; *Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Adult ; Metagenomics/methods ; East Asian People ; }, abstract = {This study aimed to characterize salivary microbiota in patients with oral cancer using 16S rRNA amplicon sequencing. DNA was extracted from saliva samples of 23 patients with oral cancer and 95 age-matched controls. A metagenomic analysis was performed using 16S rRNA amplicon sequencing. Patients with oral cancer exhibited lower α-diversity, as indicated by the Chao-1 index, compared to the control group, and significant differences in β-diversity were observed between the two groups. At the genus level, 25 bacterial species such as Lautropia, Megasphaera, Lactobacillus, Kingella, Gemella, Staphylococcus, and Propionibacterium were identified in patients with oral cancer, with more than half being Gram-positive facultative anaerobes or anaerobes. The reduced bacterial diversity in saliva of patients with oral cancer suggests dysbiosis during oral carcinogenesis may contribute to changes in bacterial distribution within the oral cavity.}, } @article {pmid40076252, year = {2025}, author = {Gao, Y and Xu, Y and Dong, Z and Guo, Y and Luo, J and Wang, F and Yan, L and Zou, X}, title = {Endophytic Fungal Diversity and Its Interaction Mechanism with Medicinal Plants.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, pmid = {40076252}, issn = {1420-3049}, support = {BS0050//Heilongjiang Province Postdoctoral Research Fund/ ; LH2022H001//Heilongjiang Natural Science Foundation Joint Guidance Project/ ; ZYW2023-073//Heilongjiang Province Traditional Chinese Medicine Research Project/ ; GZ20210110//Key Research and Development Guidance Project of Heilongjiang Province/ ; }, mesh = {*Plants, Medicinal/microbiology ; *Endophytes/metabolism/genetics/physiology ; *Fungi/metabolism/genetics/classification/physiology ; *Biodiversity ; Metabolomics ; Proteomics ; Metagenomics ; }, abstract = {This paper reviewed the diversity of endophytic fungi and their interactions with medicinal plants, along with the research methodologies utilized to investigate these interactions. It mainly includes the diversity of endophytic fungi, as well as distribution diversity, species diversity, and the diversity of their metabolites and functions, including antibacterial, anti-inflammatory, anti-tumor, insecticidal, antioxidant capabilities, and so on. The research methodologies employed to investigate the interactions between endophytic fungi and medicinal plants are categorized into metagenomics, transcriptomics, metatranscriptomics, proteomics, and metabolomics. Furthermore, this study anticipates the potential applications of secondary metabolites derived from endophytic fungi in both medicine and agriculture.}, } @article {pmid40075266, year = {2025}, author = {Cao, H and Xu, J and Wang, H and Yi, W and Yang, D and Yang, J and Sun, J and Wang, Y and Zhang, F and Yan, J and Li, D}, title = {Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {135}, pmid = {40075266}, issn = {1471-2180}, support = {2023YFF1104305//National Key Research and Development Program of China/ ; 2022YFF1100601//National Key Research and Development Program of China/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; Y2021001//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; K20221026//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; CXTD2021003//Key discipline construction program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; KX-23-C196//Soft Science Project of Wuxi Science and Technology Association/ ; YJZ202305//Medical research projects in research-oriented hospitals of Affiliated Hospital of Jiangnan University/ ; HB2023062//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023063//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023061//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; LCYJ202347//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202310//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202322//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202303//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; BK20210468//Natural Science Foundation of Jiangsu Province/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation ; Mice ; *Gastrointestinal Microbiome ; *Weight Gain ; *Liver/metabolism ; Male ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/therapy ; Lipid Metabolism ; Fatty Acids, Volatile/blood ; }, abstract = {BACKGROUND: Dysbiosis of the microbiome is strongly associated with weight rebound after dieting. However, the interactions between the host and microbiome and their relevance to the pathogenesis of post-diet weight rebound remain unclear.

PURPOSE: This study aimed to evaluate the effects of fecal microbiota transplantation (FMT) on post-diet weight regain and to investigate the underlying mechanisms by which FMT inhibits weight regain.

METHODS: FMT was administered once daily to mice for 5 weeks. Gas chromatography tandem mass spectrometry was employed to analyze short-chain fatty acid levels in serum, ultrahigh-performance liquid chromatography tandem mass spectrometry was utilized for analyzing hepatic lipid metabolites, and shotgun metagenomic sequencing was applied to examine the intestinal microbiome.

RESULTS: FMT reduced weight regain and prevented lipid accumulation in both liver and adipose tissue while also improving glucose intolerance in mice. Furthermore, FMT increased the abundance of Enterorhabdus caecimuris and decreased the abundances of Burkholderiales, Sutterellaceae, Turicimonas muris, Bacteroides stercorirosoris, and Acetivibrio ethanolgignens within the gut microbiota. Additionally, elevated propionic acid levels and significant alterations in hepatic lipid metabolites were observed following FMT administration.

CONCLUSIONS: Our findings demonstrate that FMT effectively mitigates post-diet weight regain and associated complications. These effects are mediated through interactions between the gut microbiota and the liver via the gut-propionic acid-liver axis.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40075219, year = {2025}, author = {Sun, Y and Huang, S and Li, M and Yang, Y and Ma, J and Xie, R and Wang, J and Zhao, Q and Qin, S and He, L and Jiang, J and Zhao, Q and Jin, G and Liu, X and Huang, H and Yang, Y and Wei, J and Liu, W and Wang, B and Yang, R and Su, X and Cao, H}, title = {Maternal high-fat diet disrupts intestinal mucus barrier of offspring by regulating gut immune receptor LRRC19.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {420}, pmid = {40075219}, issn = {2399-3642}, support = {82270574//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82070545//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400632//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81970488//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; *Diet, High-Fat/adverse effects ; Mice ; *Intestinal Mucosa/metabolism/immunology ; Pregnancy ; Mice, Inbred C57BL ; Indoleacetic Acids/metabolism ; Mice, Knockout ; Interleukin-22 ; Male ; Receptors, Aryl Hydrocarbon/metabolism ; Interleukins/metabolism ; *Prenatal Exposure Delayed Effects ; *Mucus/metabolism ; }, abstract = {Maternal high fat diet (MHFD) increased colitis susceptibility in adulthood. However, the mechanism remains unclear. We sought to explore whether novel gut immune receptor leucine-rich repeat C19 (LRRC19) contributed to the impaired mucus barrier of offspring exposed to MHFD via gut immune response and microbiota. The results showed that MHFD significantly impaired the intestinal mucus barrier of offspring, and up-regulated the expression of LRRC19. Lrrc19 deletion alleviated the mucus barrier disruption. Mechanistically, metagenome sequencing revealed that the MHFD-induced gut microbiota alteration was partly restored in Lrrc19[-/-] offspring. Muc2-associated bacteria were decreased in the MHFD group, such as Akkermansia_muciniphila_CAG_154, which increased in the Lrrc19-deficient offspring. Moreover, Lrrc19[-/-] offspring had a higher rate of indole-3-acetic acid (IAA)-producing bacterium, such as Lactobacillus reuteri. A targeted metabolomics analysis revealed that IAA emerged as the top candidate that might mediate the protective effects. IAA was found to improve the mucus barrier function by increasing the ratio of interleukin-22 (IL-22)[+] ILC3 cells in an aryl hydrocarbon receptor (AhR)-dependent manner. These results suggest that MHFD disrupts the intestinal mucus barrier of offspring through regulating gut immune receptor LRRC19 and inducing an imbalance of gut microbiota and microbiota-derived metabolites.}, } @article {pmid40072675, year = {2025}, author = {Verma, N and Chavan, N and Aulakh, KS and Sharma, A and Shouche, Y and Ramana, VV}, title = {Temporal Dynamics of Microbial Community Composition and Antimicrobial Resistance in a Mass Gathering Setting Using Culturomics and Metagenomic Approaches.}, journal = {Journal of epidemiology and global health}, volume = {15}, number = {1}, pages = {41}, pmid = {40072675}, issn = {2210-6014}, support = {OLP-805//CSIR - Institute of Microbial Technology/ ; GAP-233//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {India ; Metagenomics ; Humans ; *Water Microbiology ; *Microbiota ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics ; *Drug Resistance, Microbial ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the major global concerns in the current scenario. Mass-gathering events in fast-developing and densely populated areas may contribute to antibiotic resistance. Despite meticulous planning and infrastructure development, the effect of mass gatherings on microbial ecosystems and antibiotic resistance must be investigated. This study used culture and metagenome-based methods to investigate and compare the bacterial diversity, AMR profile & mechanism of resistance for bacteria in water samples collected from the mass gathering event (2019 Prayagraj Kumbh Mela in Uttar Pradesh, India) with the control samples, collected during no mass gathering.

METHODS: This study analyzed the water samples collected from a mass gathering event held in February 2019. Water samples collected in this study were grouped into "Test" (mass gathering event) and "Control" (no mass gathering event) groups. This study involved methods including culturomics, antibiotyping, phenotypic & genotypic identification methods, and metagenomics.

RESULTS: There is a significant variation observed in the evenness and richness of bacterial diversity and MDR profile, expressed in terms of the relative abundance of the bacterial species between test and control samples. Out of the total multi-drug resistant (MDR) strains identified in the Prayagraj sample, the majority were derived from the test sample. A pathway-based analysis of MDR strains revealed the highest levels of acquired resistance were related to the inhibition of cell wall synthesis primarily in Pseudomonas spp., followed by resistance to protein synthesis and nucleic acid synthesis pathways. Additionally, the overall resistance profile of the test sample demonstrated a significantly elevated resistome for beta-lactams, particularly in the Pseudomonas spp. Additionally, several ESBL (Extended-spectrum beta-lactamase)-associated gene variants were identified. The test sample showed a two-fold increase in the prevalence and diversity of common beta-lactam gene variants in addition to the presence of unique variants. Using the metagenomics approach, we investigated the mechanism of antibiotic resistance, and it revealed a dominant trend in antibiotic efflux and inactivation pathways within both the test and control samples. Overall, the bacterial diversity, abundance (including AMR strains of human origin), and ARGs were relatively higher in the Test sample compared to the control sample which was collected 3 months after the mass gathering event.

CONCLUSION: Our study found significant variations in microbial communities, MDR strains, and ARGs due to environmental and human influences. Pseudomonas spp. was the most abundant MDR strain, primarily resistant to cell wall synthesis inhibitors. The test sample showed an increased resistome for beta-lactams, while the control sample had reduced bacterial species, ARGs, and MDR strains linked to human microflora. This shift could be due to the re-establishment of native bacterial communities in the Ganges River which may be attributed to its bacteriophage activity, biomolecules, and inherent antimicrobial properties. The study highlights the need for surveillance, monitoring AMR emergence to develop new strategies to combat it.}, } @article {pmid40072088, year = {2025}, author = {Świdnicka-Siergiejko, A and Daniluk, J and Miniewska, K and Daniluk, U and Guzińska-Ustymowicz, K and Pryczynicz, A and Dąbrowska, M and Rusak, M and Ciborowski, M and Dąbrowski, A}, title = {Inflammatory Stimuli and Fecal Microbiota Transplantation Accelerate Pancreatic Carcinogenesis in Transgenic Mice, Accompanied by Changes in the Microbiota Composition.}, journal = {Cells}, volume = {14}, number = {5}, pages = {}, pmid = {40072088}, issn = {2073-4409}, support = {No NCN 2017/27/B/NZ5/02904//National Science Center/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; Mice, Transgenic ; Mice ; *Pancreatic Neoplasms/microbiology/pathology ; *Carcinogenesis/pathology ; *Inflammation/pathology/microbiology ; *Gastrointestinal Microbiome ; *Carcinoma, Pancreatic Ductal/microbiology/pathology ; Feces/microbiology ; Proto-Oncogene Proteins p21(ras)/genetics ; Male ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Female ; }, abstract = {An association between gut microbiota and the development of pancreatic ductal adenocarcinoma (PDAC) has been previously described. To better understand the bacterial microbiota changes accompanying PDAC promotion and progression stimulated by inflammation and fecal microbiota transplantation (FMT), we investigated stool and pancreatic microbiota by 16s RNA-based metagenomic analysis in mice with inducible acinar transgenic expressions of KrasG12D, and age- and sex-matched control mice that were exposed to inflammatory stimuli and fecal microbiota obtained from mice with PDAC. Time- and inflammatory-dependent stool and pancreatic bacterial composition alterations and stool alpha microbiota diversity reduction were observed only in mice with a Kras mutation that developed advanced pancreatic changes. Stool Actinobacteriota abundance and pancreatic Actinobacteriota and Bifidobacterium abundances increased. In contrast, stool abundance of Firmicutes, Verrucomicrobiota, Spirochaetota, Desulfobacterota, Butyricicoccus, Roseburia, Lachnospiraceae A2, Lachnospiraceae unclassified, and Oscillospiraceae unclassified decreased, and pancreatic detection of Alloprevotella and Oscillospiraceae uncultured was not observed. Furthermore, FMT accelerated tumorigenesis, gradually decreased the stool alpha diversity, and changed the pancreatic and stool microbial composition in mice with a Kras mutation. Specifically, the abundance of Actinobacteriota, Bifidobacterium and Faecalibaculum increased, while the abundance of genera such as Lachnospiraceace A2 and ASF356, Desulfovibrionaceace uncultured, and Roseburia has decreased. In conclusion, pancreatic carcinogenesis in the presence of an oncogenic Kras mutation stimulated by chronic inflammation and FMT dynamically changes the stool and pancreas microbiota. In particular, a decrease in stool microbiota diversity and abundance of bacteria known to be involved in short-fatty acids production were observed. PDAC mouse model can be used for further research on microbiota-PDAC interactions and towards more personalized and effective cancer therapies.}, } @article {pmid40072031, year = {2025}, author = {Huang, YJ}, title = {The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations.}, journal = {Immunological reviews}, volume = {330}, number = {1}, pages = {e70015}, pmid = {40072031}, issn = {1600-065X}, support = {U01 TR004066/TR/NCATS NIH HHS/United States ; 75N92024D00012-0-759202400001-1/HL/NHLBI NIH HHS/United States ; U01TR004066/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Asthma/microbiology/immunology/etiology ; *Microbiota/immunology ; Animals ; Disease Susceptibility ; Biomarkers ; Multiomics ; }, abstract = {Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.}, } @article {pmid40071381, year = {2025}, author = {da Silva, LP and Porto, M and Amorim, F and Beja, P and Mata, VA}, title = {Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14100}, doi = {10.1111/1755-0998.14100}, pmid = {40071381}, issn = {1755-0998}, support = {CEECIND/02064/2017//Fundação para a Ciência e a Tecnologia/ ; CEECIND/02547/2020//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1440/CP1646/CT0018//Fundação para a Ciência e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund/ ; SR20/1575//British Ecological Society/ ; }, mesh = {*Chiroptera/physiology ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics/isolation & purification ; Feces/chemistry ; *Plants/genetics/classification ; *Diet ; *Metagenomics/methods ; Arthropods ; }, abstract = {DNA metabarcoding is increasingly used in dietary studies, but it has limitations, such as detecting nonfood taxa. This issue is frequently mentioned in the literature but poorly understood, limiting interpretation of results and mitigation strategies. We evaluate the extent and sources of nonfood plant DNA in dietary metabarcoding, based on 281 faecal samples of a strictly insectivorous bat. We modelled plant taxa detections in relation to pollination syndromes, flowering and fruiting phenology and habitat associations, and we estimated co-occurrences between plants and arthropods. The bat arthropod diet was consistent with previous studies. Plants were detected in 82.9% of samples, representing 148 taxa, and all pollination syndromes evaluated. Plant detections were more frequent during their flowering periods, particularly for those with mixed pollination syndromes, suggesting a relationship between flowering and detectability. Fruiting had a positive, albeit weaker, effect. There was a tendency for more frequent detection of forest plants and less frequent detection of plants associated with riparian and agricultural habitats. Co-occurrences between arthropods and plants were weak and inconsistent. Our results highlight the potential for widespread detection of nonfood plant DNA in metabarcoding studies, calling for great care when analysing the plant component of diets. Specifically, we recommend: (i) implementing strategies for reducing plant contamination during field sampling; (ii) using multiple field and lab negative controls; and (iii) using ancillary information (e.g., sample visual inspection and literature review) to aid interpretation of metabarcoding results. Moreover, we recommend that studies reporting plant consumption results greatly diverging from dietary patterns obtained through other methods should include detailed explanations of methodological steps taken to exclude the confounding effects of nonfood plant DNA.}, } @article {pmid40069605, year = {2025}, author = {Zhang, H and Wang, Y and Luo, Z and Zhang, B and Lan, X and Xu, L and Li, X and Huang, Z and Bai, J and Hu, D}, title = {Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {128}, pmid = {40069605}, issn = {1471-2180}, support = {YC-20018//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; 2023I0046//Supported by Science and Technology Planning Project of Fujian Province, China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Forests ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; China ; Metagenomics ; Sympatry ; *Ruminants/microbiology ; DNA, Bacterial/genetics ; *Deer/microbiology ; Sequence Analysis, DNA ; Adaptation, Physiological ; }, abstract = {BACKGROUND: The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.

RESULTS: The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.

CONCLUSION: These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.}, } @article {pmid40069560, year = {2025}, author = {Breselge, S and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Cotter, PD}, title = {The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {415}, pmid = {40069560}, issn = {2399-3642}, support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; USIRL-2019-1//Science Foundation Ireland (SFI)/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine (DAFM)/ ; TC/2018/0025//Enterprise Ireland/ ; }, mesh = {*Kefir/microbiology ; Fermentation ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Metabolomics/methods ; Multiomics ; }, abstract = {Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. WK grains can be reused to start new fermentations. Here we investigate the microbial composition and function of 69 WK grains and their ferments by shotgun metagenomics. A subset of samples was subjected to metabolomic, including volatilomic, analysis. The impact of different fermentation practices on microbial composition and fermentation characteristics was analysed and it was noted that, for example, the common practice of drying water kefir grains significantly reduces microbial diversity and negatively impacts subsequent grain growth. Metagenomic analysis allowed the detection of 96 species within WK, the definition of core genera and the detection of different community states after 48 h of fermentation. A total of 485 bacterial metagenome assembled genomes were obtained and 18 putatively novel species were predicted. Metabolite and volatile analysis show associations between key species with flavour compounds. We show the complex microbial composition of WK and links between fermentation practices, microbes and the fermented product. The results can be used as a foundation for the selection of species for large scale WK production with desired flavour profiles and to guide the regulatory framework for commercial WK production.}, } @article {pmid40068786, year = {2025}, author = {Wang, L and Zhao, G and Guo, W and Li, Y and Chen, J and Niu, L}, title = {Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121363}, doi = {10.1016/j.envres.2025.121363}, pmid = {40068786}, issn = {1096-0953}, mesh = {*Estuaries ; *Sulfur/metabolism ; China ; Geologic Sediments/microbiology/chemistry ; Rivers/microbiology ; *Water Pollutants, Chemical/metabolism ; Microbiota ; *Tidal Waves ; Environmental Monitoring ; }, abstract = {Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.}, } @article {pmid40068396, year = {2025}, author = {Guo, M and Wu, Y and Huang, H and Li, S and Zhao, L and Cao, J and Wang, C}, title = {Revealing the critical role of rare bacterial communities in shaping antibiotic resistance genes in saline soils through metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137848}, doi = {10.1016/j.jhazmat.2025.137848}, pmid = {40068396}, issn = {1873-3336}, mesh = {*Soil Microbiology ; Metagenomics ; Salinity ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Salinity is considered one of the basic abiotic factors influencing the diversity and distribution of antibiotic resistance genes (ARGs) in soils, yet little is known about the distribution and driving factors of ARGs in naturally saline soils. In this study, metagenomic analysis was conducted to explore the intricate dynamics among soil salinity, microbial community structure and ARGs propagation, with a particular focus on the key contribution of rare potential-hosts of ARGs in light and heavy saline soils. The findings revealed that salinity was significantly negatively correlated with the abundance of ARGs, light saline soils hosted a greater abundance of ARGs than high saline soils, with particularly significant enrichment in genes conferring resistance to multidrug, vancomycin, bacitracin and tetracenomycin C. Proteobacteria and Actinobacteria were identified as primary hosts for ARGs. Notably, rare potential hosts of ARGs play a crucial role in shaping the abundance of ARGs despite their low relative abundance (0.85 %), significantly influencing the relative abundance of ARGs in light and heavy saline soils. The average degree of rare potential-hosts of ARGs was found to be higher in light saline soils (average degree = 45.729 and 25.923 in light and heavy saline soils, respectively), and there was stronger interaction connected between microorganisms (edges = 35,760 and 20,259 in light and heavy saline soils, respectively). Also, microbial community niche width and niche overlap of rare potential-hosts of ARGs in light saline soils were significantly greater than that in heavy saline soils. This work emphasizes the importance of bacterial communities of rare potential-hosts of ARGs on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.}, } @article {pmid40068342, year = {2025}, author = {Song, R and Lv, B and He, Z and Li, H and Wang, H}, title = {Rhizosphere metabolite dynamics in continuous cropping of vineyards: Impact on microflora diversity and co-occurrence networks.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128134}, doi = {10.1016/j.micres.2025.128134}, pmid = {40068342}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Fungi/classification/metabolism/genetics/isolation & purification ; Biodiversity ; *Vitis/microbiology/growth & development ; Soil/chemistry ; Microbiota ; Crops, Agricultural/microbiology/growth & development ; Farms ; Metabolomics ; Metagenomics ; Metabolome ; }, abstract = {The metabolism of the crop rhizosphere affects microflora diversity and nutrient cycling. However, understanding rhizosphere metabolism in suitable crops within arid desert environments and its impact on microflora interactions remains limited. Through metagenomic and non-targeted metabolomic sequencing of rhizosphere soils from one uncultivated land and four vineyards with cropping years of 5, 10, 15 and 20 years, the critical importance of rhizosphere metabolites in maintaining bacterial and fungal diversity was elucidated. The results revealed that Nocardioides, Streptomyces, and Solirubrobacter were the relatively abundant bacterial genera in rhizosphere soils, while Rhizophagus, Glomus, and Pseudogymnoascus were the relatively abundant fungal genera. The composition of rhizosphere metabolic changed significantly during the continuous cropping of grapevines. Dimethylglycine, Formononetin, and Dehydroepiandrosterone were the most important metabolites. Enrichment analysis revealed significant involvement of metabolic pathways such as biosynthesis of amino acids, unsaturated fatty acids, and linoleic acid metabolism. Procrustes analysis highlighted stronger correlations between rhizosphere metabolites and bacterial community compared to those of fungal community. This suggests distinct responses of microflora to crop-released chemical elements across different soil habitats. Co-occurrence network analysis demonstrated complex associations between rhizosphere metabolites and soil microflora, the positive correlations between rhizosphere metabolites and microflora networks predominated over negative correlations. Partial least squares path model indicated that the effect of cropping years on rhizosphere metabolites was greater than that on bacterial microflora diversity. Futhermore, pH, total phosphorus, and alkali-hydrolyzed nitrogen were the key environmental factors affecting rhizosphere metabolites and microbial diversity. These results deepen our valuable insights into the complex biological processes that rhizosphere metabolites influence on microorganisms, and provide strong support for maintaining microbial diversity in farmland soils in arid regions.}, } @article {pmid40065594, year = {2025}, author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB}, title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70272}, pmid = {40065594}, issn = {2053-1095}, support = {1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; U18 FD006716/FD/FDA HHS/United States ; W81XWH-22-1-0891//Department of Defense/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; U18 FD006993/FD/FDA HHS/United States ; //Harry M. Zweig Memorial Fund for Equine Research/ ; }, mesh = {Horses ; Animals ; *Horse Diseases/microbiology/blood ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/blood ; Male ; Female ; *Microbiota ; }, abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.

OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.

STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5°F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.

METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.

RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.

MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.

CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.}, } @article {pmid40064809, year = {2025}, author = {Ouarabi, L and Taminiau, B and Daube, G and Barache, N and Bendali, F and Drider, D and Lucau-Danila, A}, title = {Insights into fungal diversity and dynamics of vaginal mycobiota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {56}, number = {2}, pages = {1095-1101}, pmid = {40064809}, issn = {1678-4405}, support = {Alibiotech CPER/FEDER 2016-2021//Région Hauts-de-France/ ; }, mesh = {Female ; *Vagina/microbiology ; Humans ; *Fungi/classification/genetics/isolation & purification ; *Mycobiome ; Adult ; Middle Aged ; *Biodiversity ; Algeria ; Young Adult ; Metagenomics ; Phylogeny ; Microbiota ; }, abstract = {Although less studied than its bacterial counterpart, the fungal component of the vaginal microbiota plays a critical role in maintaining vaginal homeostasis. Most research on the composition of the vaginal mycobiota has focused on pathological conditions, with relatively few studies involving healthy women. To gain comprehensive insights into the vaginal mycobiota of Algerian women in two different age groups, we performed a targeted metagenomic analysis using ITS2 region sequencing data from 14 vaginal samples collected from healthy women in reproductive and postmenopausal stages. A single dominant fungal species per individual was observed in both young and postmenopausal women, with differences in fungal community composition between the two groups being related to hormone levels. Our results show that Candida and Saccharomyces were the dominant genera in both young and postmenopausal women. Notably, the postmenopausal group had twice as many species, along with the presence of uncommon taxa such as Dipodascus and Fusarium, indicating greater taxonomic diversity. These findings suggest that menopause is associated with increased microbial variability, likely due to hormonal changes that disrupt the vaginal environment. This study paves the way for more extensive analyses involving diverse age groups and ethnic backgrounds.}, } @article {pmid40064231, year = {2025}, author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y}, title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {372}, number = {}, pages = {126028}, doi = {10.1016/j.envpol.2025.126028}, pmid = {40064231}, issn = {1873-6424}, mesh = {*Oryza/microbiology ; *Microbiota/drug effects ; Plant Roots/microbiology ; Endophytes ; *Soil Pollutants/toxicity ; *Metals, Heavy ; *Bacteriophages ; Bacteria ; }, abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.}, } @article {pmid40063888, year = {2025}, author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J}, title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319461}, pmid = {40063888}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Feces/microbiology ; Female ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.}, } @article {pmid40063675, year = {2025}, author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, pmid = {40063675}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 2/microbiology/diagnosis ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; *Diabetes Mellitus, Type 1/microbiology/diagnosis ; *Bacteria/classification/genetics ; Machine Learning ; Metagenome ; Support Vector Machine ; }, abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.}, } @article {pmid40062854, year = {2025}, author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B}, title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0263924}, pmid = {40062854}, issn = {2165-0497}, support = {2022YFA1304303//National Key R&D Program of China/ ; tsqn202103196//Taishan Scholars Program of Shandong Province/ ; 82370017//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Community-Acquired Infections/microbiology/metabolism ; *Pneumonia/microbiology/metabolism ; Aged ; Metagenomics ; Metabolomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fatty Acids, Volatile/metabolism ; *Metabolome ; Bile Acids and Salts/metabolism ; Adult ; Community-Acquired Pneumonia ; }, abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.

IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.}, } @article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0298924}, pmid = {40062772}, issn = {2150-7511}, support = {T32 GM007491/GM/NIGMS NIH HHS/United States ; 5T32GM007491-46//HHS | National Institutes of Health (NIH)/ ; //Elsa U. Pardee Foundation (EUPF)/ ; }, mesh = {*Fusobacterium nucleatum/genetics/isolation & purification/classification/physiology ; Humans ; *Colorectal Neoplasms/microbiology ; Female ; Male ; *Fusobacterium Infections/microbiology ; Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Gingiva/microbiology ; Genome, Bacterial ; }, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, } @article {pmid40060112, year = {2024}, author = {Wei, B and Xu, Q and Kong, J and Su, X and Chen, K and Wang, H}, title = {Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1518637}, pmid = {40060112}, issn = {1664-462X}, abstract = {INTRODUCTION: Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays a critical role in livestock production and grassland restoration. This study investigates the rhizospheric and non-rhizospheric soil microorganisms of Poa alpigena L. in the Ganzi River area of the Qinghai Lake basin using metagenomic sequencing to understand their diversity and potential ecological functions.

METHODS: Soil samples were collected from rhizospheric and non-rhizospheric areas of Poa alpigena L. using the S-type five-point sampling method. DNA was extracted, and metagenomic sequencing was performed using the BGISEQ-500 platform. Alpha and Beta diversity analyses were conducted, and LEfSe analysis was used to identify differentially abundant microbial taxa and metabolic pathways.

RESULTS: A total of 5,681 microbial species across 1,606 genera, 521 families, 61 phyla, and 246 orders were identified. Non-rhizospheric soils exhibited higher species richness than rhizospheric soils. Proteobacteria was the most abundant phylum in both soil types. Rhizospheric soils showed significant enrichment in pathways related to antibiotic biosynthesis, carbon metabolism, and methane metabolism, while non-rhizospheric soils were enriched in quorum sensing and drug-metabolizing pathways.

DISCUSSION: The findings highlight the selective influence of Poa alpigena L. on soil microbial communities and their potential role in mitigating methane emissions. The study provides a foundation for understanding the ecological functions of soil microorganisms in alpine meadows and supports sustainable grassland management practices.}, } @article {pmid40059174, year = {2025}, author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS}, title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {71}, pmid = {40059174}, issn = {2049-2618}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; HL160862/HL/NHLBI NIH HHS/United States ; 1563159//National Science Foundation/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics/methods ; *Bacterial Adhesion/genetics ; *Bacteria/genetics/classification ; *Intestines/microbiology ; Computational Biology/methods ; Metagenome ; Promoter Regions, Genetic ; Feces/microbiology ; }, abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.

RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.

CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.}, } @article {pmid40058902, year = {2025}, author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF}, title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116035}, doi = {10.1016/j.foodres.2025.116035}, pmid = {40058902}, issn = {1873-7145}, mesh = {*Fermentation ; *Coffee/microbiology/chemistry ; *Coffea/microbiology ; Microbiota ; Food Handling/methods ; Metabolomics ; Metagenomics ; Seeds/microbiology/chemistry ; *Food Quality ; }, abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.}, } @article {pmid40058900, year = {2025}, author = {Wang, X and Li, Q and Li, W and Cai, G and Wu, D and Xie, G and Lu, J}, title = {Metagenomics unveils the roles of microbes in the metabolic network of purine formation during Huangjiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116031}, doi = {10.1016/j.foodres.2025.116031}, pmid = {40058900}, issn = {1873-7145}, mesh = {*Fermentation ; *Purines/metabolism/analysis/biosynthesis ; *Metagenomics/methods ; *Bacteria/metabolism/genetics/classification ; *Metabolic Networks and Pathways ; Microbiota ; *Fermented Foods/microbiology ; }, abstract = {Purine is a major factor contributing to the development of hyperuricemia and gout, and it is found in large quantities in Huangjiu as free bases. Purine production in Huangjiu is strongly associated with microbial metabolism. However, to the best of our knowledge the microorganisms responsible for and the mechanisms of purine formation during Huangjiu fermentation are yet to be evaluated. Herein, changes in purine levels during Huangjiu fermentation were analyzed. Further, the microbes responsible for purine production were identified and their gene abundance was studied. Results revealed that adenine, guanine, hypoxanthine, and xanthine are produced during Huangjiu fermentation. The total purines content on day 0 (27.99 mg/L) was found to be considerably lower than that produced on day 24 (122.15 mg/L) during Huangjiu fermentation. Metagenomics showed that the composition of the microbial community fluctuates sharply during five fermentation periods of Huangjiu, with the microbial community richness and diversity being the most prominent on day 3. At the genus level, Klebsiella, Lactobacillus, Staphylococcus, Saccharopolyspora, and Saccharomyces were abundant during Huangjiu fermentation and were involved in purine metabolism. Relationships between the dominant microorganisms and key enzyme genes of the purine pathways were also established based on the Kyoto Encyclopedia of Genes and Genomes database. Correlation analysis showed that Lactobacillus and Saccharomyces were the main genera involved in purine formation. Saccharomyces cerevisiae, Lactobacillus paralimentarius, and Lactiplantibacillus plantarum were involved in purine formation during Huangjiu fermentation. Overall, this study improves our understanding of the purine formation mechanism during Huangjiu fermentation and provides valuable insights into the regulation of purine formation by microorganisms.}, } @article {pmid40058443, year = {2025}, author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D}, title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.}, journal = {International journal of biological macromolecules}, volume = {307}, number = {Pt 1}, pages = {141858}, doi = {10.1016/j.ijbiomac.2025.141858}, pmid = {40058443}, issn = {1879-0003}, mesh = {Animals ; *Polysaccharides/pharmacology/chemistry ; *Osteoblasts/drug effects/metabolism ; *Osteomyelitis/drug therapy/metabolism/pathology ; Rats ; *MAP Kinase Signaling System/drug effects ; *Receptors, G-Protein-Coupled/metabolism ; Male ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Bone Regeneration/drug effects ; Disease Models, Animal ; }, abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.}, } @article {pmid40057978, year = {2025}, author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S}, title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40057978}, issn = {1751-7370}, mesh = {*Microbiota ; Single-Cell Analysis ; Transcriptome ; Gene Expression Profiling ; Photosynthesis ; Bacteria/classification/genetics ; }, abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.}, } @article {pmid40057571, year = {2025}, author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD}, title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8136}, pmid = {40057571}, issn = {2045-2322}, mesh = {Humans ; *Toothpastes/pharmacology ; Female ; *Microbiota/drug effects ; Male ; Adult ; *Dental Plaque/microbiology/drug therapy ; Double-Blind Method ; Middle Aged ; *Citrates/pharmacology ; *Zinc Compounds/pharmacology ; Young Adult ; Bacteria/classification/genetics/drug effects ; }, abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.}, } @article {pmid40057258, year = {2025}, author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP}, title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.}, journal = {Acta tropica}, volume = {264}, number = {}, pages = {107577}, doi = {10.1016/j.actatropica.2025.107577}, pmid = {40057258}, issn = {1873-6254}, mesh = {Animals ; *Triatoma/microbiology/parasitology/immunology ; *Trypanosoma cruzi/immunology ; Feces/microbiology/parasitology ; Mice, Inbred C57BL ; Mice ; *Chagas Disease/immunology/parasitology ; RNA, Ribosomal, 16S/genetics ; Cytokines ; Female ; Disease Models, Animal ; *Microbiota ; Parasite Load ; Metagenomics ; Immunoglobulin G/blood ; }, abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.}, } @article {pmid40056814, year = {2025}, author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M}, title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144296}, doi = {10.1016/j.chemosphere.2025.144296}, pmid = {40056814}, issn = {1879-1298}, mesh = {*Pesticides/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; *Organophosphates/analysis/toxicity ; Bacteria/genetics/drug effects ; Wetlands ; Lakes/microbiology/chemistry ; Genes, Bacterial ; Metals, Heavy/analysis/toxicity ; Water Microbiology ; Microbiota/drug effects ; }, abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.}, } @article {pmid40056781, year = {2025}, author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X}, title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.}, journal = {Poultry science}, volume = {104}, number = {4}, pages = {104930}, pmid = {40056781}, issn = {1525-3171}, mesh = {Animals ; *Ducks/microbiology/anatomy & histology/physiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/analysis ; *Body Size ; *Bacteria/classification/isolation & purification/genetics ; Feces/microbiology ; Male ; }, abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.}, } @article {pmid40056745, year = {2025}, author = {Zhu, S and Mao, H and Yang, X and Zhao, W and Sheng, L and Sun, S and Du, X}, title = {Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117956}, doi = {10.1016/j.ecoenv.2025.117956}, pmid = {40056745}, issn = {1090-2414}, mesh = {*Rhizosphere ; *Lead/toxicity ; *Zinc/toxicity ; *Soil Microbiology ; *Soil Pollutants/toxicity ; *Metals, Heavy/toxicity ; Mining ; *Bacteria/genetics/drug effects ; Metagenomics ; }, abstract = {This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.}, } @article {pmid40056517, year = {2025}, author = {Choonut, A and Wongfaed, N and Wongthong, L and Poolpol, A and Chaikitkaew, S and Sittijunda, S and Reungsang, A}, title = {Microbial degradation of polypropylene microplastics and concomitant polyhydroxybutyrate production: An integrated bioremediation approach with metagenomic insights.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137806}, doi = {10.1016/j.jhazmat.2025.137806}, pmid = {40056517}, issn = {1873-3336}, mesh = {*Polypropylenes/metabolism ; Biodegradation, Environmental ; *Microplastics/metabolism ; *Hydroxybutyrates/metabolism ; Microbial Consortia ; Metagenomics ; Bacteria/metabolism/genetics ; *Polyesters/metabolism ; Polyhydroxybutyrates ; }, abstract = {The persistence of plastics, particularly polypropylene (PP), and their conversion into microplastics (MPs), specifically PP-MPs, have emerged as serious ecological threats to soil and aquatic environments. In the present study, we aimed to isolate a microbial consortium capable of degrading PP-MPs. The results revealed that three microbial consortia (CPP-KKU1, CPP-KKU2, and CPP-KKU3) exhibited the ability to degrade PP-MPs, achieving weight losses ranging from 11.6 ± 0.2 % to 17.8 ± 0.5 % after 30 days. Fourier transform infrared (FTIR) spectroscopy analysis confirmed the degradation through oxidation, as evidenced by the presence of new functional groups (-OH and -C=O). In particular, CPP-KKU3 showed the highest degradation efficiency, with scanning electron microscopy (SEM) analysis revealing surface cracking after treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis identified various intermediate compounds, including heterocyclic aromatic compounds, phenyl groups, methylthio derivatives, and ethoxycarbonyl derivatives, indicating complex biochemical processes that were likely mediated by microbial enzymes. Furthermore, polyhydroxybutyrate (PHB) production by these consortia was also investigated. The result showed that both CPP-KKU2 and CPP-KKU3 successfully produced PHB, with CPP-KKU3 demonstrating superior performance in terms of PP-MP degradation and PHB production. Metagenomic analysis of CPP-KKU3 revealed abundant carbohydrate-active enzymes (CAZymes), particularly glycosyl transferases and glycoside hydrolases, which are associated with MP digestion. This study presents a promising bioremediation approach that addresses plastic waste degradation and sustainable bioplastic production, offering a potential solution for environmental plastic pollution.}, } @article {pmid40056186, year = {2025}, author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J}, title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {140}, pmid = {40056186}, issn = {1432-0851}, support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/metabolism/microbiology/immunology ; *Lung Neoplasms/drug therapy/metabolism/pathology/microbiology/immunology ; *Tryptophan/metabolism ; Female ; Male ; *Dysbiosis/metabolism/microbiology ; Middle Aged ; Aged ; Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Microbiota ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.}, } @article {pmid40055835, year = {2025}, author = {Yin, CF and Pan, P and Li, T and Song, X and Xu, Y and Zhou, NY}, title = {The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {68}, pmid = {40055835}, issn = {2049-2618}, support = {32400079//the National Natural Science Foundation of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; }, mesh = {*Acetaminophen/metabolism/analysis ; *Antipyretics/metabolism ; Metagenomics/methods ; *Aminophenols/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Wastewater/microbiology/chemistry ; China ; Humans ; *Bacteria/metabolism/genetics/classification ; Analgesics/metabolism ; COVID-19 ; Microbiota ; }, abstract = {BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.

RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20 nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68 nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.

CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.}, } @article {pmid40055808, year = {2025}, author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB}, title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {66}, pmid = {40055808}, issn = {2049-2618}, support = {2022067//Helse Sør-Øst RHF/ ; }, mesh = {*Mycobiome/genetics ; *Software ; *Metagenomics/methods ; Humans ; *Fungi/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.

RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.

CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.}, } @article {pmid40054445, year = {2025}, author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O}, title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1178-1197}, doi = {10.1016/j.cell.2025.01.038}, pmid = {40054445}, issn = {1097-4172}, mesh = {Humans ; *Microbiota ; *Big Data ; *Clinical Trials as Topic ; Animals ; Metabolomics ; Metagenomics/methods ; }, abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.}, } @article {pmid40054424, year = {2025}, author = {Ding, C and Sun, J}, title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.}, journal = {Marine environmental research}, volume = {207}, number = {}, pages = {107056}, doi = {10.1016/j.marenvres.2025.107056}, pmid = {40054424}, issn = {1879-0291}, mesh = {Indian Ocean ; *Carbon Cycle ; *Microbiota ; *Nitrogen Cycle ; Seawater/microbiology ; RNA, Ribosomal, 16S/analysis ; Bacteria ; Nitrogen Fixation ; Metagenomics ; }, abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.}, } @article {pmid40053579, year = {2025}, author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R}, title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.}, journal = {Science advances}, volume = {11}, number = {10}, pages = {eads5631}, pmid = {40053579}, issn = {2375-2548}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/genetics/metabolism ; *Gene Regulatory Networks ; *Sulfur/metabolism ; *Carbon Cycle ; *Carbon/metabolism ; Phylogeny ; Metagenome ; Genome, Bacterial ; }, abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.}, } @article {pmid40053318, year = {2025}, author = {Nihalani, R and Zola, J and Aluru, S}, title = {Disambiguating a Soft Metagenomic Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {32}, number = {5}, pages = {473-485}, doi = {10.1089/cmb.2024.0825}, pmid = {40053318}, issn = {1557-8666}, mesh = {*Metagenomics/methods ; Animals ; Cluster Analysis ; Rats ; Algorithms ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; }, abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.}, } @article {pmid40052570, year = {2025}, author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L}, title = {Multimodal metagenomic analysis reveals microbial InDels as superior biomarkers for pediatric Crohn's disease.}, journal = {Journal of Crohn's & colitis}, volume = {19}, number = {4}, pages = {}, doi = {10.1093/ecco-jcc/jjaf039}, pmid = {40052570}, issn = {1876-4479}, support = {82170542//National Natural Science Foundation of China/ ; 2021YFF0703700/2021YFF0703702//National Key Research and Development Program of China/ ; 2014008//Sun Yat-sen University Clinical Research 5010 Program/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; }, mesh = {Humans ; *Crohn Disease/microbiology/diagnosis/genetics ; *Gastrointestinal Microbiome/genetics ; Child ; *Metagenomics/methods ; *INDEL Mutation ; Feces/microbiology ; Female ; Male ; Biomarkers/analysis ; Adolescent ; Machine Learning ; }, abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1175 fecal metagenomic sequencing samples, predominantly from 3 cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1357 KEGG orthology genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1256 insertions/deletions (InDels), and 3567 single nucleotide variants, with a considerable portion of these variants located in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an area under the ROC curve (AUC) of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC = 0.996) and 5 other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of noninvasive diagnostic tools and targeted therapies.}, } @article {pmid40052474, year = {2025}, author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M}, title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {2}, pages = {e70156}, pmid = {40052474}, issn = {1541-4337}, support = {//United Arab Emirates University/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/chemistry ; *Nanoparticles/chemistry ; Humans ; *Functional Food ; }, abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.}, } @article {pmid40052450, year = {2025}, author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S}, title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2474730}, pmid = {40052450}, issn = {1365-2060}, mesh = {Humans ; *HIV Infections/drug therapy/complications/microbiology ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Middle Aged ; Adult ; Prospective Studies ; *Akkermansia/isolation & purification ; *Non-alcoholic Fatty Liver Disease/microbiology ; Feces/microbiology ; *Metabolic Diseases/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.}, } @article {pmid40052334, year = {2025}, author = {Lu, Y and Dong, Y and Zhang, M and Mao, L}, title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14095}, doi = {10.1111/1755-0998.14095}, pmid = {40052334}, issn = {1755-0998}, support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; }, mesh = {*DNA, Environmental/genetics/isolation & purification ; *Metagenome ; *Sequence Analysis, DNA/methods ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.}, } @article {pmid40050500, year = {2025}, author = {Dave, M and Tattar, R}, title = {Antimicrobial resistance genes in the oral microbiome.}, journal = {Evidence-based dentistry}, volume = {26}, number = {1}, pages = {42-43}, pmid = {40050500}, issn = {1476-5446}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; *Mouth/microbiology ; Polymerase Chain Reaction ; Systematic Reviews as Topic ; }, abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.}, } @article {pmid40050382, year = {2025}, author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q}, title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7910}, pmid = {40050382}, issn = {2045-2322}, support = {32230071//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Coleoptera/microbiology ; *Bacteria/genetics/classification ; *Weevils/microbiology ; Symbiosis ; Fungi/genetics/classification ; *Metagenome ; *Microbiota ; }, abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.}, } @article {pmid40049896, year = {2025}, author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H}, title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {550-562}, doi = {10.1016/j.jes.2024.08.026}, pmid = {40049896}, issn = {1001-0742}, mesh = {Bacteria ; *Viruses/classification ; Nitrogen/analysis ; Phosphorus/analysis ; *Water Microbiology ; *Environmental Monitoring ; RNA, Ribosomal, 16S ; Animals ; Sulfur/analysis ; Nutrients/analysis ; Water Pollutants, Chemical/analysis ; Microbiota ; }, abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.}, } @article {pmid40049354, year = {2025}, author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J}, title = {Metabolic and ecological responses of denitrifying consortia to different carbon source strategies under fluctuating C/N conditions.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121292}, doi = {10.1016/j.envres.2025.121292}, pmid = {40049354}, issn = {1096-0953}, mesh = {*Denitrification ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Microbial Consortia ; Wastewater/microbiology ; Bioreactors/microbiology ; Bacteria/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.}, } @article {pmid40048849, year = {2025}, author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK}, title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105630}, pmid = {40048849}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Metagenomics/methods ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; Female ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; }, abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.

METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.

FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.

INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.

FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.}, } @article {pmid40047424, year = {2025}, author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D}, title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {4}, pages = {e0247724}, pmid = {40047424}, issn = {1098-5336}, support = {31770540//The Natural Science Foundation of China/ ; BE2018663//The Key Research Program of Jiangsu/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Immune Tolerance ; *Hygiene ; Specific Pathogen-Free Organisms ; Feces/microbiology ; Male ; Bacteria/classification/genetics/isolation & purification ; Housing, Animal ; }, abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.

IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.}, } @article {pmid40047330, year = {2025}, author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L}, title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.}, journal = {Journal of food science}, volume = {90}, number = {3}, pages = {e70106}, doi = {10.1111/1750-3841.70106}, pmid = {40047330}, issn = {1750-3841}, support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Dextran Sulfate/adverse effects ; *Colitis/chemically induced/drug therapy/metabolism/microbiology ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Cytokines/metabolism ; Colon/metabolism/pathology/drug effects ; Intestines ; *Protein Hydrolysates ; }, abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.}, } @article {pmid40045185, year = {2025}, author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL}, title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {120}, pmid = {40045185}, issn = {1471-2180}, support = {U54 MD013368/MD/NIMHD NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; }, mesh = {California ; *Lakes/microbiology ; *Sulfur/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Microbiota ; Seasons ; *Seawater/microbiology ; Biodiversity ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.}, } @article {pmid40045177, year = {2025}, author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S}, title = {Gut microbiome in colorectal cancer: metagenomics from bench to bedside.}, journal = {JNCI cancer spectrum}, volume = {9}, number = {3}, pages = {}, pmid = {40045177}, issn = {2515-5091}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Precision Medicine ; Prognosis ; }, abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approach.}, } @article {pmid40044917, year = {2025}, author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A}, title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.}, journal = {Mycorrhiza}, volume = {35}, number = {2}, pages = {17}, pmid = {40044917}, issn = {1432-1890}, support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; }, mesh = {*Mycorrhizae/physiology/classification/genetics ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; *Plant Roots/microbiology ; Symbiosis ; *Rhizosphere ; Phosphorus/analysis ; Microbiota ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.}, } @article {pmid40044673, year = {2025}, author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G}, title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1798}, pmid = {40044673}, issn = {2041-1723}, mesh = {Animals ; *Spheniscidae/genetics/physiology ; Antarctic Regions ; *Geologic Sediments/chemistry ; DNA, Mitochondrial/genetics ; Seals, Earless/genetics ; Phylogeny ; Metagenome ; }, abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.}, } @article {pmid40043973, year = {2025}, author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X}, title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.}, journal = {International journal of biological macromolecules}, volume = {306}, number = {Pt 4}, pages = {141714}, doi = {10.1016/j.ijbiomac.2025.141714}, pmid = {40043973}, issn = {1879-0003}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Fermentation ; Fatty Acids, Volatile/metabolism ; *Auricularia/chemistry ; Feces/microbiology ; Prebiotics ; *Polysaccharides/pharmacology/metabolism ; *Fungal Polysaccharides/pharmacology/metabolism ; Bacteria/metabolism/genetics ; Metabolomics ; }, abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.}, } @article {pmid40043731, year = {2025}, author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q}, title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.}, journal = {Journal of clinical periodontology}, volume = {52}, number = {7}, pages = {1011-1023}, pmid = {40043731}, issn = {1600-051X}, support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; }, mesh = {Humans ; Female ; *Microbiota/genetics ; *Periodontitis/microbiology ; Male ; Middle Aged ; Metagenomics ; *Dysbiosis/microbiology ; *Dental Implants/microbiology ; Adult ; Periodontal Index ; Dental Plaque/microbiology ; Crowns ; }, abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.

MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.

RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.

CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.}, } @article {pmid40043390, year = {2025}, author = {Li, F and Zeng, Z and Wu, Y and Wang, Y and Shen, L and Huang, X and Wang, X and Sun, Y}, title = {Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137808}, doi = {10.1016/j.jhazmat.2025.137808}, pmid = {40043390}, issn = {1873-3336}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Microplastics/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Poultry ; Farms ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; }, abstract = {Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.}, } @article {pmid40043057, year = {2025}, author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI}, title = {What defines a photosynthetic microbial mat in western Antarctica?.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0315919}, pmid = {40043057}, issn = {1932-6203}, mesh = {Antarctic Regions ; *Photosynthesis ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; Biodiversity ; *Microbiota ; Phylogeny ; }, abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.}, } @article {pmid40042126, year = {2025}, author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB}, title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.}, journal = {Pediatric pulmonology}, volume = {60}, number = {3}, pages = {e71024}, pmid = {40042126}, issn = {1099-0496}, support = {K24 HL141669/HL/NHLBI NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; //This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; }, mesh = {Humans ; *Cystic Fibrosis/drug therapy/microbiology ; *Feces/microbiology ; Infant ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; *beta-Lactams/therapeutic use/pharmacology ; Bacterial Load ; Longitudinal Studies ; }, abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).

OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.

DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") β-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.

RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). α-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. β-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample β-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.

CONCLUSIONS: β-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.}, } @article {pmid40040609, year = {2025}, author = {Liu, FQ and An, ZY and Cui, LJ and Xiao, MY and Wu, YJ and Li, W and Zhang, BS and Yu, L and Feng, J and Liu, ZG and Feng, R and Jiang, ZX and Huang, RB and Jing, HM and Ren, JH and Zhu, XY and Cheng, YF and Li, YH and Zhou, HB and Gao, D and Liu, Y and Yu, F and Wang, X and Qiao, JL and Hu, DH and Wang, LL and Zang, MT and Chen, Q and Qu, QY and Zhou, JY and Li, ML and Chen, YX and Huang, QS and Fu, HX and Li, YY and Wang, QF and Huang, XJ and Zhang, XH and , }, title = {Correlation Between Fecal Microbiota and Corticosteroid Responsiveness in Primary Immune Thrombocytopenia: an Exploratory Study.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {22}, pages = {e2410417}, pmid = {40040609}, issn = {2198-3844}, support = {2023YFC2507803//Key Technologies Research and Development Program/ ; 82300149//National Natural Science Foundation of China/ ; 82130008//National Natural Science Foundation of China/ ; 82230004//National Natural Science Foundation of China/ ; 82350004//National Natural Science Foundation of China/ ; 82430006//National Natural Science Foundation of China/ ; 2024M761208//China Postdoctoral Science Foundation/ ; 2023ZB182//Department of Human Resources and Social Security of Jiangsu Province/ ; 2022-1-4082//Capital Health Research and Development of Special Fund/ ; 7242154//Natural Science Foundation of Beijing Municipality/ ; 7232188//Natural Science Foundation of Beijing Municipality/ ; 71003Y3035//Peking University Medicine/ ; }, mesh = {Humans ; *Purpura, Thrombocytopenic, Idiopathic/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Adrenal Cortex Hormones/therapeutic use ; Adult ; Aged ; Support Vector Machine ; Metagenomics ; Machine Learning ; }, abstract = {Corticosteroids (CSs) are the initial therapy for immune thrombocytopenia (ITP); however, their efficacy is not adequately predicted. As a novel biomarker, the composition of the gut microbiota is non-invasively tested and altered in patients with ITP. This study aims to develop a predictive model that leverages gut microbiome data to predict the CS response in patients with ITP within the initial four weeks of treatment. Metagenomic sequencing is performed on fecal samples from 212 patients with ITP, 152 of whom underwent CS treatment and follow-up. Predictive models are trained using six machine-learning algorithms, integrating clinical indices and gut microbiome data. The support vector machine (SVM) algorithm-based model has the highest accuracy (AUC = 0.80). This model utilized a comprehensive feature set that combined clinical data (including sex, age, duration, platelet count, and bleeding scales) with selected microbial species (including Bacteroides ovatus, Bacteroides xylanisolvens, and Parabacteroides gordonii), alpha diversities, KEGG pathways, and microbial modules. This study will provide new ideas for the prediction of clinical CS efficacy, enabling informed decision-making regarding the initiation of CS or personalized treatment in patients with ITP.}, } @article {pmid40038838, year = {2025}, author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K}, title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {65}, pmid = {40038838}, issn = {2049-2618}, support = {S10 OD026929/NH/NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Female ; Male ; Adult ; Skin Microbiome ; }, abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.

RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing.

CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.}, } @article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; }, mesh = {China ; *Microbiota ; *Bays/microbiology ; Archaea/genetics/classification ; Metagenome ; Bacteria/classification/genetics ; Oceans and Seas ; Metagenomics ; *Seawater/microbiology ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, } @article {pmid40038282, year = {2025}, author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and , and Brodie, EL}, title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2186}, pmid = {40038282}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; }, mesh = {*Ecosystem ; *Genomics/methods ; Methane/metabolism ; Wetlands ; *Microbiota/genetics ; Metagenomics/methods ; Climate Change ; Arctic Regions ; Bacteria/genetics/metabolism ; Greenhouse Gases/metabolism ; }, abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.}, } @article {pmid40038255, year = {2025}, author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F}, title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.}, journal = {Signal transduction and targeted therapy}, volume = {10}, number = {1}, pages = {79}, pmid = {40038255}, issn = {2059-3635}, support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Dysbiosis/microbiology/genetics/pathology ; Humans ; Mice ; *Gastrointestinal Microbiome/genetics/drug effects ; Female ; *Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/microbiology/genetics/pathology ; *Neoplastic Stem Cells/pathology/metabolism ; Wnt Signaling Pathway/genetics ; *Breast Neoplasms/microbiology/pathology/genetics ; Akkermansia ; Butyrates ; Gene Expression Regulation, Neoplastic ; }, abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.}, } @article {pmid40037607, year = {2025}, author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R}, title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.}, journal = {Letters in applied microbiology}, volume = {78}, number = {3}, pages = {}, doi = {10.1093/lambio/ovaf030}, pmid = {40037607}, issn = {1472-765X}, support = {GSBTM/JD(R&D)661/2022-2023/00172813//Gujarat State Biotechnology Mission/ ; }, mesh = {*Soil Microbiology ; Animals ; *Soil/chemistry ; Fermentation ; *Plant Development ; *Buffaloes ; *Fertilizers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Vigna/growth & development ; Feces/microbiology ; }, abstract = {This study investigates the role of microbial dynamics during the fermentation of buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after 8 days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the eighth-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.}, } @article {pmid40037564, year = {2025}, author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB}, title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.}, journal = {Age and ageing}, volume = {54}, number = {3}, pages = {}, pmid = {40037564}, issn = {1468-2834}, support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; }, mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Age Factors ; *Carrier State/microbiology ; Comorbidity ; *Homes for the Aged ; Long-Term Care ; Microbiota ; *Nursing Homes ; *Oropharynx/microbiology ; Risk Factors ; South Australia/epidemiology ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; *Staphylococcus aureus/isolation & purification ; Time Factors ; Cross-Sectional Studies ; }, abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.

OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.

METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.

RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P < .0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P < .0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P = .03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P = .04).

CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.}, } @article {pmid40037293, year = {2025}, author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG}, title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40037293}, issn = {1751-7370}, support = {DE-SC0024289//U.S. Department of Energy/ ; }, mesh = {*Methane/metabolism ; *Soil Microbiology ; California ; Desert Climate ; Microbiota ; *Ecosystem ; Metagenomics ; Metagenome ; *Plants/metabolism/microbiology ; *Bacteria/classification/metabolism/genetics ; Atmosphere/chemistry ; Oxygenases ; }, abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.}, } @article {pmid40037072, year = {2025}, author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX}, title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117976}, doi = {10.1016/j.ecoenv.2025.117976}, pmid = {40037072}, issn = {1090-2414}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Chickens/microbiology ; *Bacteria/genetics/classification ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Biodiversity ; }, abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.}, } @article {pmid40036691, year = {2025}, author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX}, title = {Benchmarking short-read metagenomics tools for removing host contamination.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40036691}, issn = {2047-217X}, support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, mesh = {*Metagenomics/methods/standards ; *DNA Contamination ; Microbiota/genetics ; Benchmarking ; Humans ; Metagenome ; Computational Biology/methods ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.

RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.

CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.}, } @article {pmid40035787, year = {2025}, author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG}, title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {49}, number = {4}, pages = {451-459}, pmid = {40035787}, issn = {1941-2444}, support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; }, mesh = {Humans ; Longitudinal Studies ; Male ; Female ; *Parenteral Nutrition ; *Gastrointestinal Microbiome ; Infant ; *Intestinal Failure/therapy/microbiology ; Child, Preschool ; Feces/microbiology ; *Weaning ; *Metabolomics ; Biomarkers/blood ; Cohort Studies ; Child ; Bacteria/classification/genetics ; Multiomics ; }, abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.

METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for ≤1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.

RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.

CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.}, } @article {pmid40032396, year = {2025}, author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA}, title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092938}, pmid = {40032396}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Switzerland ; *Sleep/physiology ; Infant ; Double-Blind Method ; *Child Development ; Child, Preschool ; Infant, Newborn ; *Synbiotics/administration & dosage ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; Birth Cohort ; Infant, Premature ; Female ; Male ; Brain ; }, abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.

METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3 months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.

ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.

TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.}, } @article {pmid40032028, year = {2025}, author = {Ismaiah, MJ and Lo, EKK and Chen, C and Tsui, JS and Johnson-Hill, WA and Felicianna, and Zhang, F and Leung, HKM and Oger, C and Durand, T and Lee, JC and El-Nezami, H}, title = {Alpha-aminobutyric acid administration suppressed visceral obesity and modulated hepatic oxidized PUFA metabolism via gut microbiota modulation.}, journal = {Free radical biology & medicine}, volume = {232}, number = {}, pages = {86-96}, doi = {10.1016/j.freeradbiomed.2025.02.029}, pmid = {40032028}, issn = {1873-4596}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Fatty Acids, Unsaturated/metabolism ; Diet, High-Fat/adverse effects ; *Liver/metabolism/drug effects/pathology ; Male ; *Obesity, Abdominal/drug therapy/metabolism/microbiology/pathology ; Lipid Metabolism/drug effects ; Mice ; Oxidation-Reduction ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: High-fat diet (HFD) is associated with visceral obesity due to disruption in the lipid metabolism and gut dysbiosis. These symptoms may contribute to hepatic steatosis and the formation of oxidized polyunsaturated fatty acids (PUFAs). Alpha-aminobutyric acid (ABA) is an amino-acid derived metabolite, and its concentration has been correlated with several metabolic conditions and gut microbiome diversity while its direct effects on visceral obesity, lipid metabolism and the gut microbiota are not well understood. This study was designed to investigate the effect of physiological dose of ABA on diet-induced visceral obesity and lipid metabolism dysregulation by examining the fatty acids and oxidized PUFAs profile in the liver as well as the gut microbiota.

RESULTS: ABA administration reduced visceral obesity by 28 % and lessened adipocyte hypertrophy. The expression of liver Cd36 was lowered by more than 50 % as well as the saturated and monounsaturated FA concentration. Notably, the desaturation index for C16 and C18 FAs that are correlated with adiposity were reduced. The concentration of several DHA-derived oxidized PUFAs were also enhanced. Faecal metagenomics sequencing revealed enriched abundance of Leptogranulimonas caecicola and Bacteroides sp. ZJ-18 and were positively correlated with several DHA- and ALA-derived oxidized PUFAs in ABA group.

CONCLUSION: Our study revealed the modulatory effect of physiological dose of ABA on attenuating visceral obesity, reducing hepatic steatosis, and promoting the production of anti-inflammatory oxidized PUFAs that were potentially mediated by the gut microbiota.}, } @article {pmid40030030, year = {2025}, author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK}, title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2413953122}, pmid = {40030030}, issn = {1091-6490}, support = {T32 AI007260/AI/NIAID NIH HHS/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; I01 CX002212/CX/CSRD VA/United States ; R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI137075/AI/NIAID NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Multiple Sclerosis/microbiology ; Animals ; Mice ; Humans ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Female ; Feces/microbiology ; Male ; Akkermansia/isolation & purification ; Adult ; Dysbiosis/microbiology ; Middle Aged ; Mice, Inbred C57BL ; Bifidobacterium/isolation & purification ; Prevotella ; Disease Models, Animal ; }, abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.}, } @article {pmid40028749, year = {2025}, author = {Salahi, A and Abd El-Ghany, WA}, title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70263}, pmid = {40028749}, issn = {2053-1095}, mesh = {*Archaea/physiology ; Animals ; Humans ; *Livestock/microbiology ; *Poultry/microbiology ; *Gastrointestinal Microbiome ; Probiotics ; }, abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.}, } @article {pmid40025399, year = {2025}, author = {Liu, A and Wu, J and Li, J and Li, Q and Zhao, N and Hu, K and Liu, S and Blaiotta, G and Zhou, J}, title = {Uncovering the microbial community dynamics and metabolic pathways of primary organic acids in Sichuan Baoning vinegar through metagenomics.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {3}, pages = {91}, pmid = {40025399}, issn = {1573-0972}, support = {No. 2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; }, mesh = {*Acetic Acid/metabolism ; *Metagenomics/methods ; Fermentation ; China ; *Metabolic Networks and Pathways ; Lactic Acid/metabolism ; *Microbiota/genetics ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Phylogeny ; Lactobacillus/metabolism/genetics ; }, abstract = {Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.}, } @article {pmid40025082, year = {2025}, author = {Regmi, R and Anderson, J and Burgess, L and Mangelson, H and Liachko, I and Vadakattu, G}, title = {Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {367}, pmid = {40025082}, issn = {2052-4463}, mesh = {*Triticum/microbiology ; *Rhizosphere ; *Microbiota ; Metagenome ; Metagenomics/methods ; *Soil Microbiology ; High-Throughput Nucleotide Sequencing ; Australia ; }, abstract = {Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned to individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements and abundance profiles across multiple samples. However, cost constraints for sequencing and limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), a DNA proximity ligation technique, has been adapted to accurately bin metagenome-assembled genomes (MAGs) from a single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data from wheat rhizospheres grown in two highly calcareous soils of South Australian region and compared conventional and Hi-C binning methods. Two shotgun metagenomes and Hi-C libraries were generated, assembling 1089 shotgun MAGs across 39 bacterial and one archaeal taxon, including 94 Hi-C based bins. Binning performed using only short read sequences was prone to high contamination, while the addition of Hi-C binning improved MAG quality and identified mobile element-host-infection interaction. This dataset provides important tools for studying microbial communities in wheat rhizosphere soils.}, } @article {pmid40024121, year = {2025}, author = {Woo, SY and Park, SB and Lee, SY and Sul, WJ and Chun, HS}, title = {Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137777}, doi = {10.1016/j.jhazmat.2025.137777}, pmid = {40024121}, issn = {1873-3336}, mesh = {*Aflatoxins/analysis ; *Microbiota ; Republic of Korea ; Aspergillus/genetics/isolation & purification ; *Glycine max/microbiology ; Penicillium/genetics ; *Food Contamination/prevention & control/analysis ; *Soy Foods/analysis/microbiology ; Fermentation ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; }, abstract = {Mycotoxin contamination is an important concern in producing traditional fermented soybean paste, though no effective control strategy has been developed. This study investigated the mycotoxin profiles of the intermediate (fermented soybean brick, known as "Meju" in South Korea) and final soybean paste products ("Doenjang") to identify major contaminants and describe microbial diversity with the mycotoxins. Profiling of 323 Meju and Doenjang samples revealed severe aflatoxin (AF) contamination. Metagenomic analysis revealed that the species richness and phylogenetic diversity were significantly higher in AF-free than in AF-contaminated Meju and Doenjang. Certain Aspergillus and Penicillium species were more abundant in AF-free than in AF-contaminated Meju and Doenjang. To control AF levels, we developed a novel mycotoxin-reduction approach that preserves the indigenous microbiome by backslopping fermentation of Meju in both Aspergillus-dominant and Penicillium-dominant modes. Both treatments reduced AF levels by > 95 % at a backslopping rate of > 2.5 %. Our results suggested that backslopping fermentation can effectively reduce AF contamination in traditional soybean fermentation, maintaining food safety standards and artisanal practices.}, } @article {pmid40023383, year = {2025}, author = {Zhang, Y and Zhang, H and Zhang, B}, title = {Biological and terrestrial influences on dissolved organic matter in Antarctic surface waters: Insights from mass spectrometry and metagenomic analysis.}, journal = {Environmental research}, volume = {273}, number = {}, pages = {121252}, doi = {10.1016/j.envres.2025.121252}, pmid = {40023383}, issn = {1096-0953}, mesh = {Antarctic Regions ; Metagenomics ; Mass Spectrometry ; *Environmental Monitoring ; *Lakes/chemistry ; Animals ; Spheniscidae ; Organic Chemicals/analysis ; }, abstract = {Global warming increases the surface waters and biodiversity in polar regions. However, the intrinsic biological sources of dissolved organic matter (DOM) in Antarctic surface waters remain poorly understood. This work evaluated the sources and driving mechanisms of DOM in Antarctic lakes systematically, based on fluorescence excitation-emission matrices, ultrahigh-resolution mass spectra, biological detection, and metagenomic analyses. The most abundant DOM in the water was peptides (37.02%), which differed from those in soil (lignins: 26.33%) and penguin guano (lipids: 50.71%). The relative abundance of CHON and CHOP compounds in water was significantly correlated with the distance from the penguin colony (p < 0.05). Both the fluorescence and mass spectrum fingerprints of water and soil/faeces showed low similarities using end-member source tracking methods. This could be attributed to the facilitation of guano-derived nutrients to phytoplankton proliferation, whereas the concentrations of NH4[+]-N, NO3[-]-N, total phosphorus, and total organic carbon were significantly higher in the penguin-intensive area than in the other areas. Algae had significant positive effects on carbohydrates and amino sugars and positive effects on lignins, compared to zooplankton and bacteria. Zooplankton had significantly more positive effects on peptides than phytoplankton. Secondary bacterial metabolic activity can be positively linked with CHO compounds. Carbohydrates and amino sugars co-occurred with carbohydrate-active enzyme genes and nitrogen cycling genes in one module of the co-occurrence network, whereas the other module was characterised by the co-occurrence patterns of condensed aromatic structures with carbohydrate-active enzyme genes and nitrogen cycling genes. These results emphasise the roles of secondary metabolites from algae and bacteria in species-specific sources of DOM, shedding light on the driving mechanisms of the biogeochemical cycling of DOM in the Antarctic water environment.}, } @article {pmid40023333, year = {2025}, author = {Liu, H and Zhou, Z and Long, C and Qing, T and Feng, B and Zhang, P and Chen, YP}, title = {Light/dark synergy enhances cyanophycin accumulation in algal-bacterial consortia: Boosted strategy for nitrogen recovery from wastewater.}, journal = {Bioresource technology}, volume = {425}, number = {}, pages = {132309}, doi = {10.1016/j.biortech.2025.132309}, pmid = {40023333}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Wastewater/chemistry/microbiology ; *Light ; *Microbial Consortia ; *Bacterial Proteins/metabolism/biosynthesis ; *Bacteria/metabolism ; }, abstract = {Recovering the nitrogen-rich biopolymer cyanophycin [(β-Asp-Arg)n] from algal-bacterial consortia enhances the reclamation of value-added chemicals from wastewater. However, the modulation of light/dark conditions on cyanophycin accumulation remain unknown. In this study, the trends and mechanisms of cyanophycin synthesis in algal-bacterial consortia under light/dark conditions were investigated. The results showed that cyanophycin production during the dark periods ranged from 137-150 mg/g MLSS (mixed liquid suspended solids), which was 32 %-38 % higher than those during the light period (p < 0.001). Metatranscriptomics results demonstrated that 50 metagenome-assembled genomes contribute to cyanophycin production, with the Planktothrix genus being the dominant contributor. Metabolomics findings suggested that algal-bacterial consortia produce higher level of arginine for cyanophycin synthesis under light conditions. This study demonstrates the feasibility of increasing cyanophycin production by merging light/dark cycles, and offers a novel strategy for high yield of valuable biopolymers from wastewater substrate.}, } @article {pmid40023235, year = {2025}, author = {Fang, J and Yin, B and Wang, X and Pan, K and Wang, WX}, title = {Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125947}, doi = {10.1016/j.envpol.2025.125947}, pmid = {40023235}, issn = {1873-6424}, mesh = {Animals ; *Geologic Sediments/chemistry ; *Mercury/metabolism/analysis ; Methylation ; *Water Pollutants, Chemical/metabolism/analysis ; *Methylmercury Compounds/analysis/metabolism ; Environmental Monitoring ; Microbiota ; Polychaeta ; }, abstract = {Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g[-1] dw d[-1]). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.}, } @article {pmid40022370, year = {2025}, author = {Li, X and You, Y and Xue, B and Chen, J and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J}, title = {Decoding microbiota and metabolite transformation in inoculated fermented suansun using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics:Impacts of different Lactobacillus plantarum strains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115847}, doi = {10.1016/j.foodres.2025.115847}, pmid = {40022370}, issn = {1873-7145}, mesh = {*Lactobacillus plantarum/metabolism/genetics ; *Metagenomics/methods ; *Metabolomics/methods ; Fermentation ; *Fermented Foods/microbiology ; Gas Chromatography-Mass Spectrometry ; *Microbiota ; Food Microbiology ; Taste ; Odorants/analysis ; }, abstract = {Using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics, we investigated the microbial communities and metabolites in two different Lactobacillus plantarum fermentations. Metagenomics revealed Weissella cibaria dominantly contributed to the DACN766-fermented suansun (LPS1) and Lactiplantibacillus pentosus to the DACN760-fermented suansun (LPS2). GC-MS identified 38 and 40 flavor compounds in LPS1 and LPS2, respectively, with p-cresol, 4-hydroxybenzaldehyde, acetic acid, hexanal, and propionic acid crucial for aroma development. LPS2 exhibited higher levels of p-cresol and acetic acid, contributing to its stronger sour and pungent flavors, which was achieved by regulating many metabolisms like glycolysis and tyrosine metabolism. In contrast, Weissella cibaria plays a role in mitigating off-flavors, resulting in a milder flavor profile in LPS1. Non-targeted metabolomics indicated 70.78% of differential metabolites were upregulated in LPS1. Conversely, the elevated expression of tryptophan and tyrosine underscores the more pronounced sour and odor-producing characteristics observed in LPS2. Metatranscriptomics highlighted the regulation of genes like XFA, XFT, and XFM, which inhibit the formation of the precursors of p-cresol and indole in LPS2. This integrated multi-omics analysis provides deep insights into the fermentation dynamics, facilitating the targeted selection of Lactobacillus plantarum strains with flavor-regulating capabilities.}, } @article {pmid40022356, year = {2025}, author = {Li, Y and Wu, Y and Chen, S and Zhao, Y and Li, C and Xiang, H and Wang, D and Wang, Y}, title = {Decoding the aroma landscape of fermented golden pompano: The interplay of ester compounds and symbiotic microbiota as revealed by metagenomics and two-dimensional flavoromics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115832}, doi = {10.1016/j.foodres.2025.115832}, pmid = {40022356}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; Fermentation ; *Esters/analysis/metabolism ; Volatile Organic Compounds/analysis ; *Odorants/analysis ; *Fermented Foods/microbiology/analysis ; Taste ; *Microbiota ; Animals ; Food Microbiology ; *Seafood/microbiology/analysis ; Flavoring Agents/analysis ; Symbiosis ; }, abstract = {Fermented pompano (Trachinotus ovatus) is a traditionally popular fermented seafood throughout Asia. Its distinctive flavor profile is primarily attributed to the microbial metabolic conversion of nutrients, which produces specific volatile compounds. Two-dimensional flavoromics of mature pompano revealed that various volatile flavor compounds accumulate throughout fermentation, with fruity (predominantly esters) and oleogustus (primarily ketones) being key flavor markers. S-curve analysis further demonstrated synergistic and additive interactions between these compounds, which enhance flavor release. Metagenomics and Kyoto Encyclopedia of Genes and Genome analysis revealed that amino acid metabolism was the pivotal pathway for ethyl ester synthesis, with Staphylococcus equorum being positively correlated with esters such as ethyl isobutyrate and ethyl enanthate. This study elucidated the interrelationship between flavor compounds and the microbial community in fermented pompano, which is expected to provide insights into flavor modulation and guide the selection of strains that produce key esters in fermented seafood products.}, } @article {pmid40022320, year = {2025}, author = {Cámara-Martos, F and Bolívar, A and Rabasco-Vílchez, L and Lafont-Déniz, F and Luque-Ojeda, JL and Pérez-Rodríguez, F}, title = {Exploring the bioaccessibility, in vitro colonic fermentation, and the impact on the intestinal microbiota of allyl-and benzyl-isothiocyanate from white and Ethiopian mustard.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115781}, doi = {10.1016/j.foodres.2025.115781}, pmid = {40022320}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Mustard Plant/chemistry ; *Fermentation ; *Isothiocyanates/metabolism/analysis/pharmacokinetics ; Ethiopia ; *Colon/microbiology/metabolism ; Digestion ; Biological Availability ; Gas Chromatography-Mass Spectrometry ; Glucosinolates/metabolism ; Humans ; *Allyl Compounds/metabolism ; Bacteria/metabolism ; }, abstract = {The aim of this research was to study the formation and bioaccessibility of allyl- and benzyl-isothiocyanate (ITC) resulting from the gastrointestinal digestion (small and large intestine) of green parts from Ethiopian and white mustard. In addition, a GC-MS methodology was validated to determine these compounds in bioaccessible and non-bioaccessible fraction. Plant clumps were divided into two batches: fresh and freeze-dried samples. ITC bioaccessibility was low in the small intestine, with values ranged between 11 and 53 % and mean values of 26 %. These results are in agreement with the fact that ITCs are poorly water-soluble compounds. Bioaccessibility values for lyophilised samples were lower than those obtained in fresh samples. This could be due to the degradation of the precursor glucosinolates (sinigrin and glucotropaeolin respectively). The simulation of the colonic fermentation reduced allyl - and benzyl - ITC levels from the non-bioaccessible fraction of Ethiopian and white mustard (values between 0.009 and 0.087 mg/g). In both cases, ITCs concentration dropped dramatically, i.e. with a ten-fold reduction. Nevertheless, this result does not necessarily indicate that ITCs have not been produced in the large intestine. Bacterial microbiota plays a key role in generating ITCs; however, ITCs are not always the final products of this process. The metagenomic analysis of colonic samples revealed that ITCs and cruciferous matrix significantly influenced the composition of gut microbiota, inhibiting potentially pathogenic bacteria such as Enterobacter and Klebsiella, while promoting beneficial bacteria such as Bifidobacterium, Faecalibacterium, Blautia, and Ruminococcus. Interestingly, ITCs-rich environments selected bacterial species (i.e. Enterobacter ludwigii) and promoted metabolic pathways involved in glucosinolate/ITCs metabolism.}, } @article {pmid40022204, year = {2025}, author = {Debray, R and Dickson, CC and Webb, SE and Archie, EA and Tung, J}, title = {Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {59}, pmid = {40022204}, issn = {2049-2618}, support = {P2C HD065563/HD/NICHD NIH HHS/United States ; R01AG071684/NH/NIH HHS/United States ; R61AG078470//National Science Foundation/ ; R01 AG071684/AG/NIA NIH HHS/United States ; R61 AG078470/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Bacteria/classification/genetics/isolation & purification ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/standards ; Papio/microbiology ; *Social Behavior ; *Environmental Microbiology ; Female ; Diet ; Rain ; }, abstract = {BACKGROUND: In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.

RESULTS: Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.

CONCLUSIONS: We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.}, } @article {pmid40022097, year = {2025}, author = {Ferneyhough, B and Roddis, M and Millington, S and Quirk, J and Clements, C and West, S and Schilizzi, R and Fischer, MD and Parkinson, NJ}, title = {A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.}, journal = {BMC urology}, volume = {25}, number = {1}, pages = {41}, pmid = {40022097}, issn = {1471-2490}, mesh = {Female ; Male ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Nanopore Sequencing/methods ; Workflow ; *Vagina/microbiology ; *Urogenital System/microbiology ; }, abstract = {BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.

RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.

CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.}, } @article {pmid40021694, year = {2025}, author = {Gambardella, N and Costa, J and Martins, BM and Folhas, D and Ribeiro, AP and Hintelmann, H and Canário, J and Magalhães, C}, title = {The role of prokaryotic mercury methylators and demethylators in Canadian Arctic thermokarst lakes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7173}, pmid = {40021694}, issn = {2045-2322}, support = {PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {*Lakes/microbiology/chemistry ; Arctic Regions ; Canada ; *Mercury/metabolism/analysis ; *Methylmercury Compounds/metabolism/analysis ; Permafrost/microbiology/chemistry ; Methylation ; Microbiota ; *Bacteria/genetics/metabolism ; Geologic Sediments/microbiology ; Metagenomics ; Seasons ; }, abstract = {Permafrost soils are critical reservoirs for mercury (Hg), with the thawing process leading to the release of this element into the environment, posing significant environmental risks. Of particular concern is the methylated form of mercury, monomethylmercury (MMHg), known for its adverse effects on Human health. Microbial communities play a pivotal role in the formation of MMHg by facilitating Hg methylation and in the demethylation of MMHg, slowing the crossing of toxic threshold concentration in the environment. However, the specific microbes involved still need to be understood. This study aimed to identify the microbial drivers behind changes in Hg speciation (MMHg and Hg) in permafrost thaw lakes and assess the significance of the biotic component in Hg biogeochemistry. Sediment samples from two thermokarst lakes in the Canadian sub-Arctic were collected during the winter and summer of 2022. Gene-centric metagenomics using whole-genome sequencing (WGS) was employed to identify key genes involved in mercury methylation (hgcA and hgcB) and demethylation (merA and merB), supported by qPCR analyses. A seasonal decline in microbial diversity, involved in the Hg methylation, and hgcA gene coverage was observed from winter to summer, mirroring patterns in mercury methylation rates. Notably, hgcA sequences were significantly more abundant than merAB sequences, with contrasting seasonal trends. These results indicate a seasonal shift in the microbial community, transitioning from a dominance of mercury methylation in winter to a predominance of mercury demethylation in summer. Environmental drivers of these dynamics were integrated into a conceptual model. This study provide new insights on the microbial processes influencing the Hg cycle in Arctic permafrost undergoing degradation.}, } @article {pmid40020468, year = {2025}, author = {Huang, Y and Li, XT and Jiang, Z and Liang, ZL and Liu, W and Liu, ZH and Li, LZ and Yang, ZN and Zhang, GQ and Yin, HQ and Liang, JL and Zhou, N and Liu, SJ and Jiang, CY}, title = {Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage.}, journal = {Water research}, volume = {278}, number = {}, pages = {123367}, doi = {10.1016/j.watres.2025.123367}, pmid = {40020468}, issn = {1879-2448}, mesh = {*Mining ; *Microbiota ; Archaea/genetics ; *Minerals ; Bacteria/genetics ; Metagenome ; Metagenomics ; }, abstract = {Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.}, } @article {pmid40020294, year = {2025}, author = {Zhao, Y and Li, L and Tan, J and Zhao, H and Wang, Y and Zhang, A and Jiang, L}, title = {Metagenomic insights into the inhibitory effect of phytochemical supplementation on antibiotic resistance genes and virulence factors in the rumen of transition dairy cows.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137717}, doi = {10.1016/j.jhazmat.2025.137717}, pmid = {40020294}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Metagenomics ; *Virulence Factors/genetics ; *Phytochemicals/pharmacology ; *Dietary Supplements ; *Drug Resistance, Microbial/genetics/drug effects ; Female ; *Flavanones/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Bacteria/genetics/drug effects ; Animal Feed ; }, abstract = {Antimicrobial resistance (AMR) is a major global health concern, with the rumen microbiota of dairy cows serving as an important reservoir for antibiotic resistance genes (ARGs) and virulence factors (VFs). This study explores the impact of dietary phytochemical supplementation on the rumen resistome and virulome of transition dairy cows using metagenomic sequencing. Naringin supplementation reduced the abundance of ARGs by up to 9.0 % and VFs by up to 7.2 % during the transition period, as indicated by metagenomic analysis (P < 0.05). Clinically high-risk ARGs, including those conferring resistance to beta-lactams (mecA), tetracyclines (tetM, tetO), and aminoglycosides (rmtF), were notably downregulated (P < 0.05). Virulence factors associated with adherence, secretion systems, and toxins were also significantly decreased (P < 0.05). Naringin altered the microbial community structure, particularly reducing the abundance of Proteobacteria, a key phylum harboring ARGs and VFs. Despite inducing increased ARG-VF network complexity, naringin supplementation promoted a less pathogenic microbiome with reduced resistance potential. These findings demonstrate the potential of naringin as a natural dietary strategy to mitigate AMR by reducing the risk of ARG and VF dissemination into the environment, while supporting rumen microbiota stability in transition dairy cows.}, } @article {pmid40020117, year = {2025}, author = {Zheng, X and Fan, J and Yin, J and Chu, Y}, title = {The role of gut microbiota and plasma metabolites in ulcerative colitis: Insights from Mendelian randomization analysis.}, journal = {Medicine}, volume = {104}, number = {9}, pages = {e41710}, pmid = {40020117}, issn = {1536-5964}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Colitis, Ulcerative/microbiology/blood/genetics ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; Middle Aged ; Longitudinal Studies ; Canada ; }, abstract = {Emerging research suggests that alterations in gut microbiota composition may play a significant role in the pathogenesis of ulcerative colitis (UC). Plasma metabolites, which are influenced by gut microbiota, have also been implicated, but their role in UC remains unclear. This study aims to determine whether specific plasma metabolites mediate the causal relationship between gut microbiota and UC using Mendelian randomization (MR) analysis. This study employed publicly available summary-level data from genome-wide association studies and metagenomic datasets. Gut microbiota data were derived from the FINRISK cohort (5959 participants), plasma metabolite data from the Canadian Longitudinal Study on Aging (8299 individuals), and UC data from multiple consortia (17,030 cases and 883,787 controls). Forward and reverse MR analyses, supplemented by linkage disequilibrium score regression (LDSC), were conducted to assess causal relationships. Mediation effects of plasma metabolites between gut microbiota and UC were analyzed using the product of coefficients method. Various sensitivity analyses, including MR-Egger and MR-PRESSO, were applied to detect pleiotropy and ensure robust results. The study identified 20 bacterial taxa and 93 plasma metabolites linked to UC. Forward MR analysis showed that Clostridium S felsineum increased UC risk via reduced carnitine levels, with a mediation proportion of 39.77%. Eubacterium callanderi was associated with decreased UC risk through the tryptophan to pyruvate ratio (16.02% mediation). Additionally, species CAG-590 sp000431135 increased UC risk through elevated mannitol/sorbitol levels, mediating 28.38% of the effect. Sensitivity analyses confirmed the robustness of these findings, with minimal heterogeneity and pleiotropy detected. This study highlights the significant role of gut microbiota and their associated plasma metabolites in the pathogenesis of UC. Specific microbial species influence UC through metabolites, suggesting potential therapeutic targets. Modulating carnitine, tryptophan metabolism, or sugar alcohols could offer promising avenues for UC management.}, } @article {pmid40019271, year = {2025}, author = {Milani, C and Longhi, G and Alessandri, G and Fontana, F and Viglioli, M and Tarracchini, C and Mancabelli, L and Lugli, GA and Petraro, S and Argentini, C and Anzalone, R and Viappiani, A and Carli, E and Vacondio, F and van Sinderen, D and Turroni, F and Mor, M and Ventura, M}, title = {Functional modulation of the human gut microbiome by bacteria vehicled by cheese.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0018025}, pmid = {40019271}, issn = {1098-5336}, support = {GR-2018-12365988//Ministero della Salute (Italy Ministry of Health)/ ; SFI/12/RC/2273a//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273b//Science Foundation Ireland (SFI)/ ; }, mesh = {*Cheese/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Feces/microbiology ; }, abstract = {Since cheese is one of the most commonly and globally consumed fermented foods, scientific investigations in recent decades have focused on determining the impact of this dairy product on human health and well-being. However, the modulatory effect exerted by the autochthonous cheese microbial community on the taxonomic composition and associated functional potential of the gut microbiota of human is still far from being fully dissected or understood. Here, through the use of an in vitro human gut-simulating cultivation model in combination with multi-omics approaches, we have shown that minor rather than dominant bacterial players of the cheese microbiota are responsible for gut microbiota modulation of cheese consumers. These include taxa from the genera Enterococcus, Bacillus, Clostridium, and Hafnia. Indeed, they contribute to expand the functional potential of the intestinal microbial ecosystem by introducing genes responsible for the production of metabolites with relevant biological activity, including genes involved in the synthesis of vitamins, short-chain fatty acids, and amino acids. Furthermore, tracing of cheese microbiota-associated bacterial strains in fecal samples from cheese consumers provided evidence of horizontal transmission events, enabling the detection of particular bacterial strains transferred from cheese to humans. Moreover, transcriptomic and metabolomic analyses of a horizontally transmitted (cheese-to-consumer) bacterial strain, i.e., Hafnia paralvei T10, cultivated in a human gut environment-simulating medium, confirmed the concept that cheese-derived bacteria may expand the functional arsenal of the consumer's gut microbiota. This highlights the functional and biologically relevant contributions of food microbes acquired through cheese consumption on the human health.IMPORTANCEDiet is universally recognized as the primary factor influencing and modulating the human intestinal microbiota both taxonomically and functionally. In this context, cheese, being a fermented food with its own microbiota, serves not only as a source of nourishment for humans, but also as a source of nutrients for the consumer's gut microbiota. Additionally, it may act as a vehicle for autochthonous food-associated microorganisms which undergo transfer from cheese to the consumer, potentially influencing host gut health. The current study highlights not only that cheese microbiota-associated bacteria can be traced in the human gut microbiota, but also that they may expand the functional repertoire of the human gut microbiota, with potentially significant implications for human health.}, } @article {pmid40018976, year = {2025}, author = {Yu, T and Gao, J and Yuan, J and Yin, Z and Chen, X and Wu, Y and Dai, R and Yan, D and Chen, H and Wu, Y}, title = {Dietary methionine restriction restores wheat gluten-induced celiac-associated small intestine damage in association with affecting butyric acid production by intestinal flora.}, journal = {Food & function}, volume = {16}, number = {6}, pages = {2461-2473}, doi = {10.1039/d4fo05757k}, pmid = {40018976}, issn = {2042-650X}, mesh = {*Methionine/metabolism/administration & dosage/deficiency ; Animals ; *Glutens/adverse effects ; *Celiac Disease/metabolism/diet therapy/microbiology ; Mice, Inbred C57BL ; Mice ; *Intestine, Small/metabolism/pathology/microbiology ; *Triticum/chemistry ; *Gastrointestinal Microbiome ; *Butyric Acid/metabolism ; Male ; Disease Models, Animal ; }, abstract = {Methionine restriction has received some attention in recent years as a novel mode of dietary intervention. Our previous study found that methionine restriction could inhibit the celiac toxic effects of wheat gluten in an in vitro model. However, the role of methionine restriction in gluten-induced celiac intestinal damage remains unclear. The aim of this study was to explore whether dietary methionine restriction could suppress the celiac toxic effects of gluten in an in vivo model, thereby mitigating intestine damage. This study systematically investigated the effects of dietary methionine restriction on celiac characteristic indicators such as symptoms, small intestine damage, and intestinal TG2 and IL-15 expression in a gluten-induced C57BL/6 mouse model. The availability of dietary methionine restriction in different ages (adolescent and adult) was also evaluated. Moreover, mouse cecum contents were assayed and co-analyzed for the metagenome of intestinal flora and target short-chain fatty acid metabolomics, with the goal of further exploring and elucidating critical pathways by which dietary methionine restriction plays a role. We discovered that dietary methionine restriction could effectively ameliorate the gluten-induced celiac-associated small intestine damage by modulating intestinal flora to inhibit butyric acid production. Specifically, dietary methionine restriction could inhibit butyric acid production with the help of s_CAG-485 sp002493045 and s_CAG-475 sp910577815, which in turn affected the mitochondrial function within the intestinal epithelial cells to assist in the repair of intestine damage. This study might provide new insights into modulating dietary patterns to mitigate intestinal damage in celiac disease and the production of novel gluten-free products.}, } @article {pmid40016914, year = {2025}, author = {Lu, X and Xu, Y and Liu, Y and Li, F and Feng, Q and Gao, C and Liu, D and Zhou, L and Yang, H and Zhang, J and Cui, F and Chen, Q}, title = {Neutrophil Depletion Reduced the Relative Abundance of Unsaturated Long-Chain Fatty Acid Synthesis Microbiota and Intestinal Lipid Absorption.}, journal = {Cell biochemistry and function}, volume = {43}, number = {3}, pages = {e70060}, doi = {10.1002/cbf.70060}, pmid = {40016914}, issn = {1099-0844}, support = {//This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Suzhou Fundamental Research Project (SJC2023001), and Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges. It was funded by the National Natural Science Foundation of China (Grant No. 81773355)./ ; }, mesh = {Animals ; Mice ; *Neutrophils/metabolism/cytology/immunology ; *Intestinal Absorption ; Male ; *Gastrointestinal Microbiome ; Lipid Metabolism ; *Fatty Acids, Unsaturated/biosynthesis ; Mice, Inbred C57BL ; Rats ; *Intestines/microbiology ; }, abstract = {As immune cells, neutrophils serve as the first line of defense against infections; however, the mechanism by which neutrophils regulate lipid metabolism is unknown. The neutrophil depletion group was treated with 100 μg InVivoMAb anti-mouse Ly6G 6 times, whereas the control group mice were intraperitoneally injected with the same quantity of InVivoMAb rat IgG2a. Body fat content, triglycerides (TGs), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) in the jejunum and ileum, as well as 9 long-chain fatty acids (LCFAs) in the intestinal contents were significantly decreased. Furthermore, genes involved in the absorption of lipids in each segment of the intestine also showed decreased expression. Neutrophil-depletion and control models were administered 25 μCi of [3]H-cholesterol by gavage. The distribution of [3]H cholesterol in the intestinal segment, heart, liver, serum, and feces was not altered by anti-Ly6G antibodies. Metagenomics was applied to investigate uncultured microorganisms in the intestinal contents to identify bacteria containing lipid metabolism genes. At the species level, 12 bacteria were involved in unsaturated LCFA synthesis, among which 2 increased and 10 decreased. The overall relative abundance of these bacteria decreased from 3.102% to 0.734%. Many genes involved in lipid metabolism were also reduced as a result, such as fatty acid synthase and peroxisome proliferator-activated receptor γ. In conclusion, neutrophil depletion does not affect intestinal lipid absorption in the diet but leads to a decrease in the overall relative abundance of gut bacteria involved in unsaturated LCFA synthesis. Consequently, intestinal lipid synthesis and absorption are reduced.}, } @article {pmid40016544, year = {2025}, author = {Zaminhan-Hassemer, M and Zagolin, GB and Aráujo, BC and Perazza, CA and Barbosa, DA and Menegidio, FB and Coutinho, LL and Tizioto, P and Hilsdorf, AWS}, title = {Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia.}, journal = {Veterinary research communications}, volume = {49}, number = {2}, pages = {120}, pmid = {40016544}, issn = {1573-7446}, mesh = {Animals ; *Propolis/pharmacology/administration & dosage/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Cichlids/growth & development/microbiology ; Dietary Supplements/analysis ; Animal Feed/analysis ; Diet/veterinary ; Bacteria/drug effects/classification ; }, abstract = {The study aimed to investigate the impact of dietary supplementation with green propolis crude extract on juvenile tilapia's growth and intestinal microbiota. The experiment was conducted in raceway tanks with a volume of 19m[3], comprising two treatments with three replicates each. Fish were assigned to either a control diet or a diet supplemented with 0.67% green propolis crude extract. Each experimental unit consisted of 30 fish, initially averaging 22.38 g ± 0.32 in weight, and which were fed ad libitum for 60 days. Results demonstrated that dietary supplementation with green propolis crude extract significantly improved the growth of juvenile tilapia compared to the control group. Firmicutes, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Cyanobacteria were identified as the predominant bacterial phyla in the intestinal microbiota of both groups. The genera Candidatus xiphinematobacter (Verrucomicrobia) and Somerae (Firmicutes) were consistently abundant across treatments, with Somerae and Dispar as the most prevalent species. Significant differences in alpha diversity were observed between treatments at the genus and species levels according to the Chao 1 index. However, no significant differences were detected in Shannon index diversity between the control and green propolis crude extract groups. Beta diversity analysis revealed distinct clustering between treatments. Linear discriminant analysis Effect Size (LEfSe) highlighted significant differences in bacterial abundance between the control and green propolis crude extract groups. In conclusion, dietary supplementation with green propolis crude extract improved growth. It also modulated the intestinal microbiota of juvenile Thai tilapia.}, } @article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism/genetics ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Nitrogen Fixation/genetics ; Soil Microbiology ; Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, } @article {pmid40015949, year = {2025}, author = {Hu, M and Xu, Y and Wang, Y and Huang, Z and Wang, L and Zeng, F and Qiu, B and Liu, Z and Yuan, P and Wan, Y and Ge, S and Zhong, D and Xiao, S and Luo, R and He, J and Sun, M and Zhuang, X and Guo, N and Cui, C and Gao, J and Zhou, H and He, X}, title = {Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway.}, journal = {Gut}, volume = {74}, number = {8}, pages = {1230-1245}, doi = {10.1136/gutjnl-2024-332891}, pmid = {40015949}, issn = {1468-3288}, mesh = {*Colorectal Neoplasms/metabolism/microbiology ; Animals ; Humans ; *Gastrointestinal Microbiome/physiology ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Muramic Acids/metabolism/pharmacology ; Male ; Signal Transduction ; Female ; Peptidoglycan/metabolism ; Disease Models, Animal ; Carcinogenesis ; Feces/chemistry/microbiology ; }, abstract = {BACKGROUND: Gut microbial metabolites are recognised as critical effector molecules that influence the development of colorectal cancer (CRC). Peptidoglycan fragments (PGFs) produced by microbiota play a crucial role in maintaining intestinal homeostasis, but their role in CRC remains unclear.

OBJECTIVE: Here, we aimed to explore the potential contribution of PGFs in intestinal tumourigenesis.

DESIGN: The relative abundance of peptidoglycan synthase and hydrolase genes was assessed by metagenomic analysis. Specific PGFs in the faeces and serum of CRC patients were quantified using targeted mass spectrometry. The effects of PGF on intestinal tumourigenesis were systematically evaluated using various murine models of CRC and organoids derived from CRC patients. Downstream molecular targets were screened and evaluated using proteome microarray, transcriptome sequencing and rescue assays.

RESULTS: Metagenomic analysis across seven independent cohorts (n=1121) revealed a comprehensive reduction in peptidoglycan synthase gene relative abundance in CRC patients. Targeted mass spectrometry identified significant depletion of a specific PGF, N-acetylmuramic acid (NAM) in CRC patients, which decreased as tumours progressed (p<0.001). NAM significantly inhibits intestinal tumourigenesis in various models, including Apc [Min/+], AOM/DSS-treated and MC38 tumour-bearing mice. Additionally, NAM inhibits the growth of patient-derived CRC organoids in a concentration-dependent manner. Mechanistically, NAM inhibits the activation of AKT1 by directly binding to it and blocking its phosphorylation, which is a partial mediator of NAM's anticancer effects.

CONCLUSION: The PGF NAM protects against intestinal tumourigenesis by targeting the AKT1 signalling pathway. NAM may serve as a novel potential preventive and therapeutic biomarker against CRC.}, } @article {pmid40015896, year = {2025}, author = {Zheng, R and Peng, J and Li, Q and Liu, Y and Huang, D and Sheng, Y and Liu, C and Qi, L and Keyhani, NO and Tang, Q}, title = {Alterations in microbial community structures and metabolic function in soil treated with biological and chemical insecticides.}, journal = {Pesticide biochemistry and physiology}, volume = {208}, number = {}, pages = {106304}, doi = {10.1016/j.pestbp.2025.106304}, pmid = {40015896}, issn = {1095-9939}, mesh = {*Soil Microbiology ; *Insecticides/pharmacology ; Neonicotinoids/pharmacology ; Metarhizium ; Nitro Compounds/pharmacology ; Ivermectin/analogs & derivatives/pharmacology ; Soil/chemistry ; *Microbiota/drug effects ; }, abstract = {Entomopathogenic fungi show significant promise as effective and ecological friendly alternatives to chemical insecticides for insect pest control. However, little is known concerning their effects on soil ecosystems, especially in comparison to application of chemical insecticides. Here, we examined the effects of one biological and two chemical insecticides, Metarhizium anisopliae, imidacloprid (IMI) and emamectin benzoate (EMB) on microbial community structure, metabolic functioning, and soil biochemistry. Treatment with EMB and IMI, reduced Actinobacteriota populations, while increasing that of Acidobacteriota. However, these populations were not significantly altered under M. anisopliae treatment. Chemical pesticides also altered fungal communities including potential pathogens. Activities of soil beneficial nitrogen-cycling-related enzymes were reduced after application of IMI and EMB, but were increased after treatment with M. anisopliae. Metagenomics analysis showed that IMI treatment reduced levels of carbon and nitrogen-related metabolic pathways. However, M. anisopliae treatment increased representation of key enzymes involved in the carbon, nitrogen, and sulfur cycling important for maintenance of soil fertility. Insecticides treatments altered the abundance of a number antibiotic resistance genes (ARGs) but not virulence factors (VFs), whereas application of M. anisopliae resulted had only minimal effects. These findings highlight the consequences of use of biological vs. chemical pesticides on soil microbiology can affect plant and ecosystem health indicating that the fungal biological control agent, M. anisopliae likely has far less detrimental and potentially beneficial effects on soil ecology as compared to chemical pesticides.}, } @article {pmid40015361, year = {2025}, author = {Liu, W and Geng, Y and Wang, Y and Zhao, J and Fan, Y and Zhang, X and Xie, W and Zhang, L and Zhang, Z}, title = {Evolution of gut microbiota in psoriatic arthritis treated with IL-17 inhibitor revealed by metagenomics.}, journal = {Joint bone spine}, volume = {92}, number = {4}, pages = {105868}, doi = {10.1016/j.jbspin.2025.105868}, pmid = {40015361}, issn = {1778-7254}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; *Arthritis, Psoriatic/drug therapy/microbiology/diagnosis ; *Interleukin-17/antagonists & inhibitors ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Feces/microbiology ; Treatment Outcome ; Adult ; Aged ; }, abstract = {OBJECTIVES: To explore the evolution of gut microbiota in taxonomy and function in PsA patients during IL-17i treatment.

METHODS: Twenty PsA patients treated with secukizumab were included. Fecal samples were collected before treatment (0 mo.), first month (1 mo.) and third month (3 mo.) after treatment, and a total of 60 samples were collected. Shotgun metagenomic sequencing was used to detect all fecal samples.

RESULTS: In the 1 mo. and 3 mo. after IL-17i treatment, the disease activity in PsA patients decreased significantly. Compared with 0 mo., α-diversity calculated by Shannon index and Pielou index increased significantly at 1 mo. and 3 mo. after treatment. Microbial genes encoding Carbohydrate-Active enZymes (CAZymes) tended to be upregulated after treatment. After treatment, Bacteroidota phylum expanded, especially the abundance of Phocaeicola genus increased gradually with the treatment time (P<0.05). The abundance of Phocaeicola genus was positively correlated with the α-diversity. The Polysaccharide Lyases and Carbohydrate Esterases in CAZymes were significantly positively correlated with most of species in Phocaeicola genus.

CONCLUSIONS: Treatment with IL-17i induces gut microbiota evolution in PsA patients. The key features of this evolution include increased α-diversity, expansion of the Phocaeicola genus, and upregulation of CAZymes. Species within the Phocaeicola genus may be the critical bacteria driving this evolution.}, } @article {pmid40015021, year = {2025}, author = {Velásquez-Reyes, D and García-Alamilla, P and Kirchmayr, MR and Lugo-Cervantes, E and Gschaedler, A}, title = {Contribution of post-harvest processing in cocoa bean: Chemometric and metagenomic analysis in fermentation step.}, journal = {Food chemistry}, volume = {477}, number = {}, pages = {143458}, doi = {10.1016/j.foodchem.2025.143458}, pmid = {40015021}, issn = {1873-7072}, mesh = {*Cacao/chemistry/microbiology/metabolism ; Fermentation ; *Bacteria/genetics/isolation & purification/metabolism/classification ; Volatile Organic Compounds/metabolism/chemistry/analysis ; Metagenomics ; Mexico ; Food Handling/methods ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Chemometrics ; Fungi/isolation & purification/classification/metabolism/genetics ; Odorants/analysis ; }, abstract = {Cocoa fermentation is a heterogeneous process, exhibiting a high degree of diversity of flavor, aroma, and microbial communities. A study was conducted to examine cocoa fermentations in five municipalities of a region in Mexico, with the objective of associating post-harvest practices, geographic area, and chemical and microbiological profiles. Through the application of high-performance DNA sequencing, the microbial diversity was identified, and the non-volatile and volatile compounds were identified and quantified by UHPLC-RID/PDA and HS-SPME/GC-MS, respectively. Using PCA, PLS regression and Pearson correlation, post-harvest practices, geographical factors, microbial communities, and volatile and non-volatile compounds were made. The absence of control in cocoa fermentation was associated to Aspergillus, Escherichia, and Bacillus, and reduced the production of essential acids for aroma. This study provides data on the diversity of post-harvest practices and their impact on cocoa quality.}, } @article {pmid40013797, year = {2025}, author = {Bai, Y and Hu, Y and Chen, X and Hu, L and Wu, K and Liang, S and Zheng, J and Gänzle, MG and Chen, C}, title = {Comparative metagenome-associated analysis of gut microbiota and antibiotic resistance genes in acute gastrointestinal injury patients with the risk of in-hospital mortality.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0144424}, pmid = {40013797}, issn = {2379-5077}, support = {200221115835503//the Office of Talent Work Leading Group in Maoming/ ; 2022A1515220065//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Hospital Mortality ; *Metagenome/genetics ; Aged ; *Drug Resistance, Microbial/genetics ; Prospective Studies ; Metagenomics/methods ; *Gastrointestinal Diseases/microbiology/mortality ; Feces/microbiology ; Intensive Care Units ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; }, abstract = {UNLABELLED: Acute gastrointestinal injury (AGI) is known for its poor long-term prognosis and the associated increase in mortality among intensive care unit (ICU) patients. As the role of the gut microbiome and resistome in AGI remains unclear, the present study aimed to explore the possible associations between dysbacteriosis and in-hospital mortality in ICU patients with gastrointestinal dysfunction. Fecal samples were collected from a prospective cohort of 210 ICU patients with AGI, and shotgun metagenomic sequencing was used to determine the taxonomic composition of gut microbiota and the differences of antibiotic resistance genes (ARGs) between the Death and Survival groups. Compared to the Survival group, patients in the Death group shifted from strict anaerobes to facultative anaerobes in the fecal microbial community, with more Klebsiella but less Prevotella. The co-occurrence patterns revealed that more ARG subtypes were enriched in microbial taxa in the Death group, especially for Clostridium and Methanobrevibacter. Furthermore, the ARG type had large area under the curve (AUCs) in receiver operating characteristic for predicting the disease severity, and a combined gut microbiota-ARG subtype classifiers showed better performance than either of them. Thus, comparative metagenome-associated analysis can help to obtain valuable information about gut microbiota and gene coding for antibiotic resistance in AGI patients.

IMPORTANCE: A metagenomic-related strategy was conducted to obtain a highly valuable resource to improve understanding of intestinal microbiota dysbiosis and antibiotic resistance genes (ARGs) profiles. The results indicate that intestinal microbiota, including Klebsiella and Prevotella, changed dramatically in intensive care unit (ICU) patients with acute gastrointestinal injury (AGI). Due to longer ICU stays and receiving more antibiotic treatment, the types and correlations of ARGs in the Death group were significantly higher than those in the Survival group. The findings of this study are expected to expand our knowledge of gut microbiota and resistome profiles reflecting gastrointestinal status, accelerate the identification of disease biomarkers, and provide new insights into the prevention and treatment of AGI-related diseases.}, } @article {pmid40013792, year = {2025}, author = {Qin, Y and Wang, Q and Lin, Q and Liu, F and Pan, X and Wei, C and Chen, J and Huang, T and Fang, M and Yang, W and Pan, L}, title = {Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0080524}, pmid = {40013792}, issn = {2379-5077}, support = {AD22035214//Guangxi Clinical Research Center for Anesthesiology/ ; 2022GXNSFAA035510//National Science Foundation of Guangxi/ ; 8236080196//National Science Foundation of China/ ; 81760530//National Science Foundation of China/ ; 2021M693803//Postdoctoral Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colonic Neoplasms/microbiology/genetics ; *Transcriptome ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Bacteria/genetics/classification ; Metagenomics ; Multiomics ; }, abstract = {UNLABELLED: Colon cancer (CC) is one of the most common cancers globally, which is associated with the gut microbiota intimately. In current research, exploring the complex interaction between microbiomes and CC is a hotspot. However, the information on microbiomes in most previous studies is based on fecal, which does not fully display the microbial environment of CC. Herein, we collected mucosal and tissue samples from both the tumor and normal regions of 19 CC patients and clarified the composition of mucosal microbiota by 16S rRNA and metagenomic sequencing. Additionally, RNA-Seq was also conducted to identify the different expression genes between tumor and normal tissue samples. We revealed significantly different microbial community structures and expression profiles to CC. Depending on correlation analysis, we demonstrated that 1,472 genes were significantly correlated with CC tumor microbiota. Our study reveals a significant enrichment of Campylobacter jejuni in the mucosa of CC, which correlates with bile secretion. Additionally, we observe a negative correlation between C. jejuni and immune cells CD4+ Tem and mast cells. Finally, we discovered that metabolic bacterial endosymbiont of Bathymodiolus sp., Bacillus wiedmannii, and Mycobacterium tuberculosis had a significant survival value for CC, which was ignored by previous research. Overall, our study expands the understanding of the complex interplay between microbiota and CC and provides new targets for the treatment of CC.

IMPORTANCE: This study contributes to our understanding of the interaction between microbiota and colon cancer (CC). By examining mucosal and tissue samples rather than solely relying on fecal samples, we have uncovered previously unknown aspects of CC-associated microbiota. Our findings reveal distinct microbial community structures and gene expression profiles correlated with CC progression. Notably, the enrichment of Campylobacter jejuni in CC mucosa, linked to bile secretion, underscores potential mechanisms in CC pathogenesis. Additionally, observed correlations between microbial taxa and immune cell populations offer new avenues for immunotherapy research in CC. Importantly, this study introduces CC-associated microbiota with survival implications for CC, expanding therapeutic targets beyond conventional strategies. By elucidating these correlations, our study not only contributes to uncovering the potential role of gut microbiota in colon cancer but also establishes a foundation for mechanistic studies of gut microbiota in colon cancer, emphasizing the broader impact of microbiota research on cancer biology.}, } @article {pmid40013791, year = {2025}, author = {Walter, JM and Greses, S and Hagen, LH and Schiml, VC and Pope, PB and González-Fernández, C and Arntzen, M}, title = {Anaerobic digestion of microalgae: microbial response and recovery after organic loading disturbances.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0167424}, pmid = {40013791}, issn = {2379-5077}, support = {101007006//EC | Horizon 2020 Framework Programme (H2020)/ ; 295910//Norges Forskningsråd (Forskningsrådet)/ ; }, mesh = {*Microalgae/metabolism ; Anaerobiosis ; *Bioreactors/microbiology ; Methane/metabolism ; Microbiota ; Fermentation ; Biofuels ; RNA, Ribosomal, 16S/genetics ; }, abstract = {UNLABELLED: Industrial anaerobic digestion (AD) represents a relevant energy source beyond today's fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, which is frequently caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure. Here, we investigate the effect of the microalgal organic loading rate (OLR) on the fermentation product profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics, and metagenome-centric metaproteomics. Both low- and high-ORL fed systems encountered a sudden decline in methane production during OLR disturbances, followed by a recovery of the methanogenic activity within the microbiome. In the high-OLR disturbances, system failure triggered an upregulation of hydrolytic enzymes, an accumulation of fermentation products, and a shift in the methanogenic population from hydrogenotrophic to acetoclastic methanogens, with the latter being essential for recovery of the system after collapse.

IMPORTANCE: Anaerobic digestion (AD) with microalgae holds great potential for sustainable energy production, but process instability caused by substrate disturbances remains a significant barrier. This study highlights the importance of understanding the microbial dynamics and system responses during organic loading rate perturbations. By identifying key shifts in microbial populations and enzyme activity, particularly the transition from hydrogenotrophic to acetoclastic methanogens during recovery, this research provides critical insights for improving AD system stability and can contribute to optimizing microalgae-based AD processes for more reliable and efficient methane production.}, } @article {pmid40013331, year = {2025}, author = {Standley, JM and Marcelino, J and Yu, F and Ellis, JD}, title = {A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14090}, doi = {10.1111/1755-0998.14090}, pmid = {40013331}, issn = {1755-0998}, support = {//University of Florida Entomology and Nematology Gahan Endowment/ ; //Clay County Beekeepers Association/ ; 1019945//USDA/NIFA Multi-State Project/ ; AP22PPQS&T00C189//USDA/APHIS Cooperative Agreement/ ; }, mesh = {Animals ; Bees/microbiology/virology/metabolism ; *Metagenomics/methods ; *Fatty Acids/metabolism ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; Virome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.}, } @article {pmid40011766, year = {2025}, author = {Proctor, DM and Sansom, SE and Deming, C and Conlan, S and Blaustein, RA and Atkins, TK and , and Dangana, T and Fukuda, C and Thotapalli, L and Kong, HH and Lin, MY and Hayden, MK and Segre, JA}, title = {Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes.}, journal = {Nature}, volume = {639}, number = {8056}, pages = {1016-1023}, pmid = {40011766}, issn = {1476-4687}, mesh = {*Nursing Homes/statistics & numerical data ; Humans ; *Skin/microbiology ; *Candida auris/genetics/isolation & purification/drug effects/classification ; Metagenomics ; beta-Lactamases/genetics ; Male ; Female ; Aged ; Microbiota/genetics ; Aged, 80 and over ; Bacteria/isolation & purification/genetics/drug effects ; Bacterial Proteins ; }, abstract = {Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings[1]. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions[2]. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.}, } @article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, } @article {pmid40007605, year = {2025}, author = {Buffet-Bataillon, S and Durão, G and Le Huërou-Luron, I and Rué, O and Le Cunff, Y and Cattoir, V and Bouguen, G}, title = {Gut microbiota dysfunction in Crohn's disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1540352}, pmid = {40007605}, issn = {2235-2988}, mesh = {Humans ; *Crohn Disease/microbiology/pathology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Male ; *Bacteria/classification/genetics/isolation & purification ; Female ; Adult ; Middle Aged ; Dysbiosis ; Virulence Factors ; }, abstract = {INTRODUCTION: Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.

METHODS: We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.

RESULTS: As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.

CONCLUSIONS: This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.}, } @article {pmid40006931, year = {2025}, author = {Sarker, S and Talukder, S and Athukorala, A and Whiteley, PL}, title = {The Spleen Virome of Australia's Endemic Platypus Is Dominated by Highly Diverse Papillomaviruses.}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, pmid = {40006931}, issn = {1999-4915}, mesh = {Animals ; Phylogeny ; *Virome ; Genome, Viral ; Australia ; *Platypus/virology ; *Papillomaviridae/genetics/classification/isolation & purification ; *Spleen/virology ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Evolution, Molecular ; }, abstract = {The platypus (Ornithorhynchus anatinus), a unique monotreme, represents a pivotal point in mammalian evolution with its distinctive traits, such as electroreception and venom production. Despite its evolutionary significance, the viral diversity within platypuses remains poorly understood. This study employed next-generation sequencing to investigate the virome of the dead platypuses, uncovering a range of novel and divergent viruses. Among the identified viruses were four complete genomes of papillomaviruses (OaPV1-4) exhibiting substantial divergence from known strains, suggesting a novel genus within the subfamily Secondpapillomavirinae. Additionally, five novel parvoviruses were detected, including two with complete genomes, highlighting the complex viral ecosystem of the platypus. Phylogenetic analysis placed these viruses in unique evolutionary branches, further demonstrating the platypus's evolutionary significance. A circular DNA virus, a tombus-like virus, and a nodamuvirus were also identified, expanding the understanding of viral diversity in monotremes. These findings offer crucial insights into viral evolution in one of the most unique mammalian lineages, emphasising the need for further exploration to assess ecological and pathological impacts on platypus populations.}, } @article {pmid40005640, year = {2025}, author = {Cao, X and Cui, Q and Li, D and Liu, Y and Liu, K and Li, Z}, title = {Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005640}, issn = {2076-2607}, support = {2022YSKY-57//Integrated analysis of soil hydrologic function of returning farmland to forest (grass) in Basic Scientific Research Youth Exploration Project of Central public welfare research Institute of Chinese Research Academy of Environmental Sciences, China/ ; }, abstract = {The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustainable use of land resources are key to addressing its ecological challenges. Soil microbial communities are vital to ecosystem functioning, and land use is a major human factor influencing their structure and diversity. Existing research on the Huanghe alluvial plain primarily focuses on soil physicochemical properties and moisture content, with relatively limited attention given to soil microorganisms. Therefore, this study, using the Wudi Tanyang Forest Farm in the Huanghe alluvial plain as a case study, employs high-throughput metagenomic sequencing to analyze the composition and diversity of soil bacteria, eukaryota, archaea, and virus communities in five different land use types (Tamarix chinensis forest, Fraxinus chinensis forest, farmland, wetland, and grassland). The results indicate that: (1) At the phylum level, the top three bacteria communities were Pseudomonadota, Acidobacteriota, and Actinomycetota; the top three in the eukaryota communities were Ascomycota, Mucoromycota, and Basidiomycotina; the top three in the archaea communities were Nitrososphaerota, Euryarchaeota, and Candidatus Thermoplasmatota; and the virus communities were dominated by Uroviricota; (2) The microbial community structure of the Tamarix chinensis forest and the Fraxinus chinensis forest was similar, and was significantly different from the other three land use types; (3) The land use type had a significant effect on the diversity of the soil microbial communities, with a higher diversity in the wetland and grassland soils; (4) The dominant species of the soil microbial communities under different land use types showed significant differences. This study provides theoretical support for land use optimization and sustainable soil management in the Huanghe alluvial plain region.}, } @article {pmid40005401, year = {2025}, author = {Straume, Z and Krūmiņa, N and Elbere, I and Rozenberga, M and Erts, R and Rudzīte, D and Proskurina, A and Krumina, A}, title = {Impact of Vitamins, Antibiotics, Probiotics, and History of COVID-19 on the Gut Microbiome in Ulcerative Colitis Patients: A Cross-Sectional Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {2}, pages = {}, pmid = {40005401}, issn = {1648-9144}, support = {1.1.1.1/21/A/029//the European Regional Development Fund (ERDF)/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/drug therapy ; Female ; Cross-Sectional Studies ; Male ; *Gastrointestinal Microbiome/drug effects ; *COVID-19/complications/epidemiology ; *Vitamins/therapeutic use ; *Anti-Bacterial Agents/therapeutic use ; Adult ; Middle Aged ; *Probiotics/therapeutic use ; SARS-CoV-2 ; }, abstract = {Background and Objectives: The human gut microbiome is essential for the health of the host and is affected by antibiotics and coronavirus disease 2019 (COVID-19). The gut microbiome is recognized as a contributing factor in the development of ulcerative colitis. Specific vitamins and probiotics have been demonstrated to positively influence the microbiome by enhancing the prevalence of expected beneficial microorganisms. Materials and Methods: Forty-nine ulcerative colitis (UC) outpatients from Riga East Clinical University Hospital were enrolled in this cross-sectional study from June 2021 to December 2021. All patients were divided into groups based on history of COVID-19 (COVID-19 positive vs. COVID-19 negative) in the last six months. Information about antibiotic, probiotic, and vitamin intake were outlined, and faecal samples were collected. The MetaPhlAn v.2.6.0 tool was used for the taxonomic classification of the gut microbiome metagenome data. Statistical analysis was performed using R 4.2.1. Results: Of the 49 patients enrolled, 31 (63%) were male and 18 (37%) were female. Coronavirus disease 2019 was found in 14 (28.6%) patients in the last 6 months. Verrucomicrobia was statistically significantly lower in the COVID-19 positive group (M = 0.05; SD = 0.11) compared to the COVID-19 negative group (M = 0.5; SD = 1.22), p = 0.03. Antibiotic non-users had more Firmicutes in their microbiome than antibiotic users (p = 0.008). The most used vitamin supplement was vitamin D (N = 18), fifteen (42.9%) of the patients were COVID-19 negative and 3 (21.4%) were COVID-19 positive over the last six months (p > 0.05). Vitamin C users had more Firmicutes in their gut microbiome compared to non-users (Md = 72.8 [IQR: 66.6; 78.7] vs. Md = 60.1 [IQR: 42.4; 67.7]), p = 0.01. Conclusions: Antibiotic non-users had more Firmicutes than antibiotic users in their gut microbiome. Only vitamin C had statistically significant results; in users, more Firmicutes were observed. A mild course of COVID-19 may not influence ulcerative colitis patients' gut microbiome.}, } @article {pmid40005052, year = {2025}, author = {Zang, P and Chen, P and Chen, J and Sun, J and Lan, H and Dong, H and Liu, W and Xu, N and Wang, W and Hou, L and Sun, B and Zhang, L and Huang, J and Wang, P and Ren, F and Liu, S}, title = {Alteration of Gastrointestinal Function and the Ameliorative Effects of Hericium erinaceus Polysaccharides in Tail Suspension Rats.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, pmid = {40005052}, issn = {2072-6643}, support = {242300421105//Henan Natural Science Foundation of Excellent Young Scholars/ ; }, mesh = {Animals ; Rats, Sprague-Dawley ; Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Hericium/chemistry ; *Hindlimb Suspension/adverse effects ; Weightlessness Simulation/adverse effects ; *Polysaccharides/pharmacology ; *Gastrointestinal Tract/drug effects ; Dietary Supplements ; *Gastrointestinal Diseases/prevention & control/etiology ; Metagenomics ; Dysbiosis ; Metabolomics ; }, abstract = {Background/Objectives: Long-term spaceflight in a microgravity environment frequently results in gastrointestinal dysfunction, presenting substantial challenges to astronauts' health. Hericium erinaceus, a plant recognized for its dual use as food and medicine, contains a key functional component called Hericium erinaceus polysaccharide (HEP), which is purported to promote gastrointestinal health. This study aims to investigate the protective effects of HEP against gastrointestinal disturbances induced by simulated weightlessness and to elucidate its regulatory mechanisms. Methods: Sprague Dawley rats subjected to a tail suspension model were administered either a standard diet or a diet supplemented with 0.125% HEP over a period of 4 weeks (the intake of HEP is approximately 157.5 mg/kg bw/d, n = 8), metagenomics and targeted metabolomics to investigate the effects of HEP on gastrointestinal hormone secretion disorders, gut microbiota dysbiosis, and intestinal barrier damage induced by simulated weightlessness. Results: Dietary supplementation with HEP was observed to significantly alleviate weightlessness-induced gastrointestinal hormone disruptions, enhancing motility and intestinal barrier function while reducing inflammation. In addition, HEP improved gut microbiota by boosting beneficial bacteria as Oscillibacter sp.1-3, Firmicutes bacterium ASF500, and Lactobacillus reuteri, while reducing harmful bacteria like Escherichia coli and Mucispirillum schaedleri at the species level. Furthermore, HEP altered the serum metabolic profile of the rats, reducing inflammation by upregulating the tryptophan metabolism pathway and enhancing the production of short-chain fatty acids. Conclusions: HEP effectively protects against gastrointestinal dysfunction induced by simulated weightlessness by regulating hormone secretion and maintaining intestinal homeostasis.}, } @article {pmid40004244, year = {2025}, author = {Blankestijn, JM and Baalbaki, N and Beijers, RJHCG and Cornelissen, MEB and Wiersinga, WJ and Abdel-Aziz, MI and Maitland-van der Zee, AH and , }, title = {Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, pmid = {40004244}, issn = {1422-0067}, support = {LSHM20104; LSHM20068//Health Holland/ ; }, mesh = {Humans ; *COVID-19/microbiology ; *Feces/microbiology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; SARS-CoV-2/isolation & purification ; Adult ; }, abstract = {An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut-lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV1, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID.}, } @article {pmid40004174, year = {2025}, author = {Cui, Y and Guan, H and Okyere, SK and Hua, Z and Deng, Y and Deng, H and Ren, Z and Deng, J}, title = {Microbial Guardians or Foes? Metagenomics Reveal Association of Gut Microbiota in Intestinal Toxicity Caused by DON in Mice.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, pmid = {40004174}, issn = {1422-0067}, support = {. 32273072//This research was supported by National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Trichothecenes/toxicity ; *Metagenomics/methods ; Cytokines/metabolism/genetics ; Male ; Jejunum/pathology/drug effects/metabolism/microbiology ; Colon/pathology/drug effects/metabolism/microbiology ; Intestinal Mucosa/metabolism/pathology/drug effects ; Zonula Occludens-1 Protein/metabolism ; *Intestines/drug effects/pathology/microbiology ; }, abstract = {The role of gut microbiota has become a research hotspot in recent years; however, whether the gut microbiota are involved in the alleviation or exacerbation of Deoxynivalenol (DON) toxicity has not been fully studied. Therefore, the objective of this study was to investigate whether the gut microbiota are involved in reducing or aggravating the intestinal damage induced by DON in mice. Mice that received or did not receive antibiotic-induced intestinal flora clearance were orally given DON (5 mg kg/bw/day) for 14 days. At the end of the experiment, serum, intestinal tissue samples and colon contents were collected for further analysis. DON caused development of severe histopathological damage, such as necrosis and inflammation of the jejunum and colon in mice without gut microbiota clearance. The levels of tight junction proteins ZO-1 and occludin were reduced in the jejunum and colon of mice without gut microbiota clearance. In addition, the mRNA and protein levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) were increased in mice without gut microbiota clearance. The presence of microbiota exacerbate the intestinal damage induced by DON via changes in gut microbiota abundance and production of gut damaging metabolites.}, } @article {pmid40003915, year = {2025}, author = {Chao, X and Fan, Z and Wu, J and Ye, C and Wang, X and Li, R and Chen, S and Zhang, X and Fang, C and Luo, Q}, title = {Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, pmid = {40003915}, issn = {1422-0067}, support = {2022B0202100002//Key-Area Research and Development Program of Guangdong Province/ ; 2024B03J1353//Science and Technology Program of Guangzhou City/ ; 2023ZD04064//STI2030-Major Projects/ ; }, mesh = {Animals ; *Chickens/microbiology/genetics ; *Poultry Diseases/microbiology/genetics ; *Salmonella Infections, Animal/microbiology/genetics ; *Metagenomics/methods ; *Salmonella/genetics ; Gastrointestinal Microbiome/genetics ; *RNA, Messenger/genetics ; RNA-Seq ; Cecum/microbiology ; Alternative Splicing ; Gene Expression Profiling ; }, abstract = {The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.}, } @article {pmid40003912, year = {2025}, author = {Chatzokou, D and Tsarna, E and Davouti, E and Siristatidis, CS and Christopoulou, S and Spanakis, N and Tsakris, A and Christopoulos, P}, title = {Semen Microbiome, Male Infertility, and Reproductive Health.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, pmid = {40003912}, issn = {1422-0067}, mesh = {Male ; Humans ; *Infertility, Male/microbiology ; *Semen/microbiology ; *Reproductive Health ; *Microbiota ; Spermatozoa/microbiology ; Female ; Pregnancy ; Semen Analysis ; }, abstract = {The semen microbiome, once believed to be sterile, is now recognized as a dynamic ecosystem containing a diverse range of microorganisms with potential implications for male fertility and reproductive health. We aimed to examine the relationship between the semen microbiome, male infertility, and reproductive outcomes, highlighting the transformative role of next generation sequencing techniques and bioinformatics in exploring this intricate interaction, and we present a critical review of the published literature on this issue. Current evidence suggests a complex association between the composition of the semen microbiome and male fertility, with certain bacterial genera, such as Lactobacillus and Prevotella that exert opposing effects on sperm quality and DNA integrity. In addition, the influence of the semen microbiome extends beyond natural fertility, affecting assisted reproductive technologies and pregnancy outcomes. Despite considerable progress, challenges remain in standardizing methodologies and interpreting findings. In conclusion, we identify the lack of a definitive management proposal for couples presenting with this phenomenon, and we underline the need for an algorithm and indicate the questions raised that point toward our goal for a strategy. Continued research is essential to clarify the role of the semen microbiome in male reproductive health and to advance the development of personalized fertility management approaches.}, } @article {pmid40000989, year = {2025}, author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P}, title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {90}, pmid = {40000989}, issn = {1471-2180}, support = {32201393//National Natural Science Foundation of China/ ; }, mesh = {*Helicobacter pylori/drug effects/genetics ; Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Feces/microbiology ; Mutation ; Metagenomics ; Female ; Evolution, Molecular ; Male ; Bacteria/genetics/classification/drug effects ; Middle Aged ; Genome, Bacterial ; Adult ; Klebsiella/genetics/drug effects ; }, abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.}, } @article {pmid39999861, year = {2025}, author = {Mejia, G and Jara-Servin, A and Hernández-Álvarez, C and Romero-Chora, L and Peimbert, M and Cruz-Ortega, R and Alcaraz, LD}, title = {Rhizosphere microbiome influence on tomato growth under low-nutrient settings.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {3}, pages = {}, pmid = {39999861}, issn = {1574-6941}, support = {DGAPA-PAPIIT-UNAM IN206824//Universidad Nacional Autónoma de México/ ; }, mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology/growth & development ; *Nutrients/metabolism ; Biomass ; }, abstract = {Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.}, } @article {pmid39999339, year = {2025}, author = {Hohmann, M and Iliasov, D and Larralde, M and Johannes, W and Janßen, KP and Zeller, G and Mascher, T and Gulder, TAM}, title = {Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles.}, journal = {ACS synthetic biology}, volume = {14}, number = {3}, pages = {967-978}, pmid = {39999339}, issn = {2161-5063}, mesh = {*Thiazoles/pharmacology/metabolism/chemistry ; *Anti-Bacterial Agents/pharmacology/metabolism/chemistry ; Humans ; Gastrointestinal Microbiome ; *Bacteroidetes/genetics/metabolism ; }, abstract = {Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.}, } @article {pmid39998665, year = {2025}, author = {Szóstak, N and Budnik, M and Tomela, K and Handschuh, L and Samelak-Czajka, A and Pietrzak, B and Schmidt, M and Kaczmarek, M and Galus, Ł and Mackiewicz, J and Mackiewicz, A and Kozlowski, P and Philips, A}, title = {Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {110}, pmid = {39998665}, issn = {1432-0851}, support = {2017/25/B/NZ5/01949//Narodowe Centrum Nauki/ ; POIR.04.01.02-00-0025/17-00//Narodowe Centrum Badań i Rozwoju/ ; }, mesh = {Humans ; *Melanoma/drug therapy/immunology/microbiology/pathology ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; *Lymphocytes/immunology ; Middle Aged ; Aged ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Mycobiome/immunology ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Adult ; Aged, 80 and over ; }, abstract = {Research has shown that the microbiome can influence how the immune system responds to melanoma cells, affecting the course of the disease and the outcome of the therapy. Here, we used the metagenomic approach and flow cytometry analyses of blood cells to discover correlations between gut fungi of metastatic melanoma patients enrolled in anti-PD-1 therapy and lymphocytes in their blood.We analyzed the patterns of associations before the first administration of anti-PD-1 therapy (BT, n = 61) and in the third month of the therapy (T3, n = 37), allowing us to track changes during treatment. To understand the possible impact of gut fungi on the efficacy of anti-PD-1 therapy, we analyzed the associations in clinical beneficiaries (CB, n = 37) and non-beneficiaries (NB, n = 24), as well as responders (R, n = 28) and non-responders (NR, n = 33).Patients with LDH < 338 units/L, overall survival (OS) > 12, CB, as well as R, had lower levels of Shannon diversity (p = 0.02, p = 0.05, p = 0.05, and p = 0.03, respectively). We found that the correlation pattern between intestinal fungi and lymphocytes was specific to the type of response, positive or negative. When comparing CB and NB groups, correlations with opposite directions were detected for C. albicans, suggesting a response-specific immune reaction. For CB, M. restricta exhibited a set of correlations with different types of lymphocytes, with prevalent positive correlations, suggesting a robust immune response in the CB group. This result extends our former research, where M. restricta and C. albicans were associated with an increased risk of melanoma progression and a poorer response to anti-PD-1 treatment.}, } @article {pmid39998261, year = {2025}, author = {Woh, PY and Chen, Y and Kumpitsch, C and Mohammadzadeh, R and Schmidt, L and Moissl-Eichinger, C}, title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0218324}, pmid = {39998261}, issn = {2165-0497}, support = {F83, P32697, COE7//Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; *Multiple Sclerosis/microbiology/drug therapy ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; Male ; Aged ; *Archaea/classification/genetics/metabolism/isolation & purification ; Methanobrevibacter/genetics/isolation & purification/metabolism/classification ; Metagenomics ; Methane/metabolism ; }, abstract = {The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically Methanobrevibacter species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (n = 21), fingolimod (n = 20), glatiramer acetate (n = 14), interferon (n = 18), natalizumab (n = 6), or ocrelizumab/rituximab (n = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of Methanobrevibacter smithii and M. sp900766745 compared to untreated patients. Notably, M. sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for M. smithii and M. sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.}, } @article {pmid39998243, year = {2025}, author = {Brochu, HN and Zhang, Q and Song, K and Wang, L and Deare, EA and Williams, JD and Icenhour, CR and Iyer, LK}, title = {Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.}, journal = {Microbiology spectrum}, volume = {13}, number = {4}, pages = {e0258224}, pmid = {39998243}, issn = {2165-0497}, mesh = {Female ; *Vaginosis, Bacterial/microbiology/diagnosis ; Humans ; *Vagina/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Adult ; Actinobacteria ; }, abstract = {Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.}, } @article {pmid39998226, year = {2025}, author = {Martino, C and Kellman, BP and Sandoval, DR and Clausen, TM and Cooper, R and Benjdia, A and Soualmia, F and Clark, AE and Garretson, AF and Marotz, CA and Song, SJ and Wandro, S and Zaramela, LS and Salido, RA and Zhu, Q and Armingol, E and Vázquez-Baeza, Y and McDonald, D and Sorrentino, JT and Taylor, B and Belda-Ferre, P and Das, P and Ali, F and Liang, C and Zhang, Y and Schifanella, L and Covizzi, A and Lai, A and Riva, A and Basting, C and Broedlow, CA and Havulinna, AS and Jousilahti, P and Estaki, M and Kosciolek, T and Kuplicki, R and Victor, TA and Paulus, MP and Savage, KE and Benbow, JL and Spielfogel, ES and Anderson, CAM and Martinez, ME and Lacey, JV and Huang, S and Haiminen, N and Parida, L and Kim, H-C and Gilbert, JA and Sweeney, DA and Allard, SM and Swafford, AD and Cheng, S and Inouye, M and Niiranen, T and Jain, M and Salomaa, V and Zengler, K and Klatt, NR and Hasty, J and Berteau, O and Carlin, AF and Esko, JD and Lewis, NE and Knight, R}, title = {SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0401524}, pmid = {39998226}, issn = {2150-7511}, support = {R01 GM069811/GM/NIGMS NIH HHS/United States ; NNF20SA0066621//Novo Nordisk Foundation/ ; R01 ES027595/ES/NIEHS NIH HHS/United States ; 1P30DK120515//HHS | National Institutes of Health (NIH)/ ; U19 AI116497/AI/NIAID NIH HHS/United States ; R00RG2503//UC | University of California, San Diego (UCSD)/ ; 2031989//National Science Foundation (NSF)/ ; ANR-17-CE11-0014//French National Research Agency/ ; 335525//Academy of Finland/ ; 3022//Emerald Foundation/ ; 1DP1AT010885//HHS | National Institutes of Health (NIH)/ ; U01 CA199277/CA/NCI NIH HHS/United States ; R01-CA077398//HHS | National Institutes of Health (NIH)/ ; R01ES027595//HHS | National Institutes of Health (NIH)/ ; UM1 CA164917/CA/NCI NIH HHS/United States ; R01GM069811//HHS | National Institutes of Health (NIH)/ ; RG/18/13/33946//British Heart Foundation (BHF)/ ; 2018-72190270//ANID Becas Chile Doctorado/ ; //Emil Aaltosen Säätiö (Emil Aaltonen Foundation)/ ; UH2AI153029//HHS | National Institutes of Health (NIH)/ ; //Health Data Research UK (HDR UK)/ ; AI Horizons Network//IBM | IBM Research/ ; P30-CA023100//HHS | National Institutes of Health (NIH)/ ; P30-CA033572//HHS | National Institutes of Health (NIH)/ ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; //NIHR | NIHR Cambridge Biomedical Research Centre (NIHR Cambridge BRC)/ ; //Sydäntutkimussäätiö (Finnish Foundation for Cardiovascular Research)/ ; UH2 AI153029/AI/NIAID NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; 101046041//Union's Horizon Europe Research and Innovation 459 Actions/ ; //Munz Chair of Cardiovascular Prediction and Prevention/ ; 321351 and 354447//Academy of Finland/ ; R35GM119850//HHS | National Institutes of Health (NIH)/ ; UM1-CA164917//HHS | National Institutes of Health (NIH)/ ; P30 CA023100/CA/NCI NIH HHS/United States ; R01 CA077398/CA/NCI NIH HHS/United States ; BRC-1215-20014//NIHR | NIHR Cambridge Biomedical Research Centre (NIHR Cambridge BRC)/ ; R35 GM119850/GM/NIGMS NIH HHS/United States ; RG/13/13/30194//British Heart Foundation (BHF)/ ; P30 CA033572/CA/NCI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 2038509//National Science Foundation (NSF)/ ; N/A//UC San Diego Center for Microbiome Innovation/ ; P01 HL131474/HL/NHLBI NIH HHS/United States ; U01-CA199277//HHS | National Institutes of Health (NIH)/ ; 321356//Academy of Finland/ ; //Alfred Benzon Foundation (The Alfred Benzon Foundation)/ ; ANR-20-CE44-0005//French National Research Agency/ ; }, mesh = {Humans ; *COVID-19/virology/microbiology/metabolism ; *Glycocalyx/metabolism/virology ; *SARS-CoV-2/pathogenicity/physiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Heparan Sulfate Proteoglycans/metabolism ; Middle Aged ; Gastrointestinal Tract/microbiology ; Adult ; *Bacteria/metabolism ; Spike Glycoprotein, Coronavirus/metabolism ; }, abstract = {The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract's glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2's spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity in vitro. Moreover, we engineered the common probiotic Escherichia coli Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.}, } @article {pmid39997957, year = {2025}, author = {Muhie, S and Gautam, A and Mylroie, J and Sowe, B and Campbell, R and Perkins, EJ and Hammamieh, R and Garcia-Reyero, N}, title = {Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics.}, journal = {Toxics}, volume = {13}, number = {2}, pages = {}, pmid = {39997957}, issn = {2305-6304}, abstract = {Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.}, } @article {pmid39997213, year = {2025}, author = {Calado, R and Leal, MC and Silva, RXG and Borba, M and Ferro, A and Almeida, M and Madeira, D and Vieira, H}, title = {Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery.}, journal = {Marine drugs}, volume = {23}, number = {2}, pages = {}, pmid = {39997213}, issn = {1660-3397}, support = {UIDB/50017/2020 + UIDP/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; (Project Nº. C644915664-00000026)//"BLUE BIOECONOMY PACT", co-funded by the Next Gen-eration EU European Fund, under the incentive line "Agendas for Business Innovation" within Component 5-Capitalization and Business Innovation of the Portuguese Recovery and Resili-ence Plan (RRP), specifi/ ; }, mesh = {Animals ; *Anthozoa/metabolism ; *Biological Specimen Banks ; Coral Reefs ; *Bioprospecting/methods ; *Biological Products ; }, abstract = {Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and this is currently hampered by multiple ethical and technological constraints. Living coral displays, research laboratories, and biobanks currently offer an opportunity to continue to unravel coral chemodiversity, acting as "Noah's Arks" that may continue to support the bioprospecting of molecules of interest. This issue is even more relevant if one considers that tropical coral reefs currently face unprecedent threats and irreversible losses that may impair the biodiscovery of molecules with potential for new products, processes, and services. Living coral displays provide controlled environments for studying corals and producing both known and new metabolites under varied conditions, and they are not prone to common bottlenecks associated with bioprospecting in natural coral reefs, such as loss of the source and replicability. Research laboratories may focus on a particular coral species or bioactive compound using corals that were cultured ex situ, although they may differ from wild conspecifics in metabolite production both in quantitative and qualitative terms. Biobanks collect and preserve coral specimens, tissues, cells, and/or information (e.g., genes, associated microorganisms), which offers a plethora of data to support the study of bioactive compounds' mode of action without having to cope with issues related to access, standardization, and regulatory compliance. Bioprospecting in these settings faces several challenges and opportunities. On one hand, it is difficult to ensure the complexity of highly biodiverse ecosystems that shape the production and chemodiversity of corals. On the other hand, it is possible to maximize biomass production and fine tune the synthesis of metabolites of interest under highly controlled environments. Collaborative efforts are needed to overcome barriers and foster opportunities to fully harness the chemodiversity of tropical corals before in-depth knowledge of this pool of metabolites is irreversibly lost due to tropical coral reefs' degradation.}, } @article {pmid39995022, year = {2025}, author = {Thangavel, M and Sneha, MJX and Mani, I and Surendrababu, A and Rajapriya, P and Arulselvan, P and Alarfaj, AA and Thangavelu, I and Pandi, M}, title = {Diversity of Endophytic Fungi in Plant Species: Traditional vs. High-Throughput Sequencing Approaches.}, journal = {Chemistry & biodiversity}, volume = {22}, number = {6}, pages = {e202402792}, doi = {10.1002/cbdv.202402792}, pmid = {39995022}, issn = {1612-1880}, mesh = {*High-Throughput Nucleotide Sequencing ; *Endophytes/genetics/isolation & purification/classification ; *Fungi/genetics/isolation & purification/classification ; Phylogeny ; Plant Leaves/microbiology ; Biodiversity ; }, abstract = {The plant microbiome significantly impacts plant life, with fungi playing a crucial role in shaping interactions and classifications. Advances in cultivation technologies have refined fungal classification, and research highlights the vital connection between endophytic fungi and their plant hosts. The present study employs morphological and phylogenetic techniques, predicting the Internal Transcribed Spacer 2 (ITS2) secondary structure and using next-generation sequencing (NGS) data to detect fungal endophytes in plant leaves via both traditional and conventional approaches. The research area, with its hot semi-arid environment and red and black soils, supports drought-resistant plants like Senna auriculata, Ziziphus mauritiana, and Catunaregam spinosa, known for their medicinal properties. These plants, rich in antioxidants, play a vital role in traditional medicine and highlight the region's rich ethno-botanical heritage. The culture-dependent study on the foliage yielded a total of 17 isolates from S. auriculata and 16 each from both C. spinosa and Z. mauritiana. The most common genera, Alternaria and Nigrospora, account for 18.3% of all isolated endophytic fungi. Three plants were colonized with Nigrospora and Lasiodiplodia, and their morphotypes were determined using ITS2 secondary structure prediction. Recent ecological studies highlight unculturable taxa, or dark taxa, where many species cannot sporulate or be cultured, emphasizing the need for High - Throughput Sequencing (HTS) approaches. The study gathered 68,791 reads from S. auriculata with 101 operational taxonomic units (OTUs), 58,620 from C. spinosa with 219 OTUs, and 66,087 from Z. mauritiana with 193 OTUs, with the majority of OTUs related to Colletotrichum (69%) and a minimum of Myrmaecium (2%). A total of 49 fungal isolates were obtained from traditional methods, whereas 513 fungal OTUs were retrieved through HTS methods, confirming the presence of a highly abundant fungus population in plant samples. The study reveals that using the ITS short amplicon sequencing technique provides distinct insights into endophytic fungal communities in three plant samples. In conclusion, analyzing plant fungal components using a combination of culture-dependent and culture-independent techniques may be a novel strategy.}, } @article {pmid39993154, year = {2025}, author = {Yang, K and Zhang, L and Ruiz-Valencia, A and Song, X and Vogel, TM and Zhang, X}, title = {Heterogeneity in the Composition and Catabolism of Indigenous Microbiomes in Subsurface Soils Cocontaminated with BTEX and Chlorinated Aliphatic Hydrocarbons.}, journal = {Environmental science & technology}, volume = {59}, number = {9}, pages = {4540-4550}, doi = {10.1021/acs.est.4c10071}, pmid = {39993154}, issn = {1520-5851}, mesh = {*Microbiota ; *Soil Microbiology ; Biodegradation, Environmental ; Soil Pollutants ; Benzene ; Toluene ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Benzene Derivatives ; Xylenes ; Hydrocarbons, Chlorinated ; }, abstract = {The effectiveness of in situ bioremediation can be affected by an insufficient understanding of high site/soil heterogeneity, especially in cocontaminated soils and sediments. In this study, samples from multiple locations within a relatively small area (20 × 20 m[2]) contaminated with benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) were compared to examine their physicochemical and microbial properties. Unsupervised clustering analysis of 16S rRNA gene amplicon and metagenome shotgun sequencing data indicates that the indigenous community differentiated into three distinct patterns. In Cluster 1, Pseudomonas, with multiple monooxygenases and glutathione S-transferase (GST), was enriched in samples contaminated with high concentrations of BTEX and CAHs. Cluster 2 contained a high fraction of cometabolic degraders. Cluster 3 was dominated by Ralstonia and organohalide-respiring bacteria (OHRBs) mediating the reductive dechlorination of CAHs. Significant differences in composition and function among microbiomes were attributed to the differential distribution of organic pollutants, even in such a small area. Incorporating genomic features with physicochemical data can significantly enhance the understanding of the heterogeneities in soil and their impacts on microbial communities, thereby providing valuable information for the optimization of bioremediation strategies.}, } @article {pmid39992132, year = {2025}, author = {Rodríguez-Ramos, J and Sadler, N and Zegeye, EK and Farris, Y and Purvine, S and Couvillion, S and Nelson, WC and Hofmockel, KS}, title = {Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation.}, journal = {mSystems}, volume = {10}, number = {3}, pages = {e0161624}, pmid = {39992132}, issn = {2379-5077}, support = {FWP 70880//Department of Energy, Office of Science, Genomic Sciences Program/ ; 60461//DOE | SC | PNNL | Environmental Molecular Sciences Laboratory (EMSL)/ ; 508623//Joint Genome Institute (JGI)/ ; }, mesh = {*Soil Microbiology ; Porosity ; *Soil/chemistry ; Phenotype ; Chitin/metabolism ; Microbiota ; Microbial Consortia ; Water ; Streptomyces/metabolism ; Metabolome ; Metagenome ; }, abstract = {Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.}, } @article {pmid39991687, year = {2025}, author = {Pan, Y and Jiao, FY}, title = {Helicobacter pylori infection and gastric microbiota: Insights into gastric and duodenal ulcer development.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100044}, pmid = {39991687}, issn = {2219-2840}, mesh = {Humans ; *Duodenal Ulcer/microbiology/pathology ; Gastric Mucosa/microbiology/pathology ; *Gastrointestinal Microbiome ; *Helicobacter Infections/microbiology/complications ; *Helicobacter pylori/pathogenicity/isolation & purification ; *Stomach Ulcer/microbiology/pathology ; Review Literature as Topic ; }, abstract = {Helicobacter pylori (H. pylori) infection plays a critical role in gastric diseases, impacting the microbiota structure in gastric and duodenal ulcers. In their study, Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls, revealing significant changes in microbial diversity and composition. This article reviews their findings, emphasizing H. pylori's role in gastric ulcers and the need for further research on its impact on duodenal ulcers. We evaluate the study's strengths and limitations, suggesting future research directions to enhance our understanding of H. pylori's contribution to ulcerative diseases.}, } @article {pmid39991683, year = {2025}, author = {Darnindro, N and Abdullah, M and Sukartini, N and Rumende, CM and Pitarini, A and Nursyirwan, SA and Fauzi, A and Makmun, D and Nelwan, EJ and Shatri, H and Rinaldi, I and Tanadi, C}, title = {Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100051}, pmid = {39991683}, issn = {2219-2840}, mesh = {Humans ; Indonesia/epidemiology ; Male ; Middle Aged ; Female ; *Colorectal Neoplasms/microbiology/pathology ; Case-Control Studies ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; Colonoscopy ; Aged ; *Intestinal Mucosa/microbiology ; *Colon/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide. Several studies have shown an association between gut microbiota and colorectal cancer. Gut microbiota is unique and can be influenced by geographic factors and habits. This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.

AIM: To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.

METHODS: This case-control study included 59 subjects (35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr. Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital. Microbiota examination was performed using 16S rRNA sequencing. Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs (Oxford Nanopore Technologies platform).

RESULTS: Patients with colorectal cancer had a higher median index value on the Shannon index (3.28 vs 2.82, P > 0.05) and a lower value on the Simpson index (0.050 vs 0.060, P > 0.05). Significant differences in beta diversity were observed at the genus (P = 0.002) and species levels (P = 0.001). Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the dominant phyla. The genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found more frequently in colorectal cancer, while Faecalibacterium, Haemophilus, and Phocaeicola were more frequently found in non-colorectal cancer. The relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Enterococcus faecalis, Campylobacter hominis, and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer. Meanwhile, Faecalibacterium prausnitzii, Faecalibacterium duncaniae, and Prevotella copri were more commonly found in non-colorectal cancer.

CONCLUSION: Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer. This study was reviewed and approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia (No. KET-1517/UN2.F1/ETIK/PPM.00.02/2023).}, } @article {pmid39987648, year = {2025}, author = {Zampieri, A and Carraro, L and Mohammadpour, H and Rovere, GD and Milan, M and Fasolato, L and Cardazzo, B}, title = {Presence and characterization of the human pathogenic Vibrio species in the microbiota of Manila clams using cultural and molecular methods.}, journal = {International journal of food microbiology}, volume = {433}, number = {}, pages = {111113}, doi = {10.1016/j.ijfoodmicro.2025.111113}, pmid = {39987648}, issn = {1879-3460}, mesh = {Animals ; *Bivalvia/microbiology ; *Vibrio/isolation & purification/genetics/classification ; *Microbiota ; *Shellfish/microbiology ; Humans ; Metagenomics ; Food Contamination/analysis ; }, abstract = {The North Adriatic lagoons and the Po River Delta are important areas for farming Manila clams (Ruditapes philippinarum). These areas have been heavily impacted by climate change, reducing livestock numbers and increasing pathogen spread. Shellfish, particularly clams, are primary vectors for Vibrio pathogens affecting humans. In this study, the occurrence of human pathogenic Vibrio species on Manila clams was investigated using an integrated approach that combined culture-dependent and culture-independent techniques. Samples were collected over three years from farming areas in the northeastern Adriatic lagoons and the Po River Delta, regions seriously impacted by climate change and pollution. In this study, species of the human pathogen Vibrio were analyzed in the clam microbiota and characterized using recA-pyrH metabarcoding and shotgun metagenomics. Human pathogenic Vibrio species were widespread in the clam microbiota, especially in summer, demonstrating that the environmental conditions on the northern Adriatic coasts allowed the growth of these bacteria. V. parahaemolyticus and V. vulnificus were also quantified using qPCR in <50 % of summer samples Shotgun metagenomics revealed the similarity of V. parahaemolyticus strains to other worldwide genomes, enabling improved pathogen identification and tracking. In the future, climate change could cause these conditions to become even more favorable to these bacteria, potentially increasing pathogen spread. Consequently, enhanced monitoring and control of both the environment and seafood products should be planned to ensure food safety.}, } @article {pmid39986751, year = {2025}, author = {Wang, C and Zhao, J and Zhao, W and Xue, L and Chen, Y and Tian, J and Wang, H and Ji, X and Tian, X and Zhang, J and Gu, Y}, title = {A comparative study of the composition of microorganisms and metabolites in different β-casein genetic types of dairy cows based on metagenomics and non-targeted metabolomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {204}, number = {}, pages = {115859}, doi = {10.1016/j.foodres.2025.115859}, pmid = {39986751}, issn = {1873-7145}, mesh = {Animals ; Cattle ; *Caseins/genetics/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Female ; *Gastrointestinal Microbiome ; *Rumen/microbiology/metabolism ; Milk/chemistry ; Arachidonic Acid/metabolism ; *Bacteria/classification/metabolism/genetics ; Genotype ; }, abstract = {β-Casein is the main component of cow's milk protein, with A1 and A2 β-casein being the most common. Of these, A1 β-casein hydrolysate produces BCM-7, which can cause lactose intolerance, while A2 β-casein milk is more gentle on the gut. However, there is limited research on the composition of rumen microbiota, metabolites, and host metabolites in different genotype cows using metagenomics and metabolomics. In this study, we used multi-omics analysis techniques to perform enrichment analysis of differential metabolites, identifying three key metabolic pathways in all three groups: Arachidonic acid metabolism and Tryptophan metabolism. The metabolites in these pathways exhibited unique metabolic characteristics within each group. We then used random forests and ROC to predict key metabolites in these pathways, identifying that the signature metabolites in the A2A2 group were predominantly anti-inflammatory substances, including 12-HETE, PGD2-4d, and Arachidonic Acid. The signature metabolites in the A1A2 group and A2A2 group were Indoleacetaldehyde. The AUC of these signature metabolites was greater than 0.85. Macrogenic linear discriminant analysis (LDA > 2.5) found that the microorganisms with greater contribution were concentrated in the A2A2 group. Compared with the other two groups, g_Bacteroides and g_Parabacteroides were mainly enriched in the A1A2 group. In group A2A2, g_Xanthomonas and g_Acetobacter are mainly enriched. Then, the key microorganisms in A1A2 group were identified by correlation analysis as g_Bacteroides and g_Parabacteroides. The key microorganisms in group A2A2 were g_Acetobacter, g_Xanthomonas and g_Mannheimia, which were consistent with the results of LEfSe analysis. These microorganisms mainly affect the degradation of fiber in the diet, host metabolism and the occurrence of inflammation. In conclusion, our results provide theoretical basis and data support for the study of dairy cows with different genotypes of β-casein, and help to determine the potential biological functions of different genotypes of casein in dairy products and their effects on human health.}, } @article {pmid39986042, year = {2025}, author = {Bacha, LF and Oliveira, MAP and Landuci, F and Vicente, AC and Paz, PH and Lima, M and Hilá